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data preparation" +authors = [ + "Nikola Rados", + "Sangwon Lim", + "Cairo Sanders", + "James Hiebert Date: Fri, 24 May 2024 14:47:09 -0700 Subject: [PATCH 02/32] Update Makefile --- Makefile | 45 ++++++++++++++++++--------------------------- 1 file changed, 18 insertions(+), 27 deletions(-) diff --git a/Makefile b/Makefile index 793ed8b..cdc0e8e 100644 --- a/Makefile +++ b/Makefile @@ -1,10 +1,6 @@ # Configuration APP_ROOT := $(abspath $(lastword $(MAKEFILE_LIST))/..) APP_NAME := thunderbird -VENV?=/tmp/thunderbird-venv -PYTHON=${VENV}/bin/python3 -PIP=${VENV}/bin/pip -export PIP_INDEX_URL=https://pypi.pacificclimate.org/simple # Notebook targets LOCAL_URL = http://localhost:5000 @@ -13,7 +9,7 @@ DEV_PORT ?= $(shell bash -c 'read -ep "Target port: " port; echo $$port') # Used in target refresh-notebooks to make it looks like the notebooks have # been refreshed from the production server below instead of from the local dev # instance so the notebooks can also be used as tutorial notebooks. -OUTPUT_URL = https://docker-dev03.pcic.uvic.ca/wpsoutputs +OUTPUT_URL = https://marble-dev01.pcic.uvic.ca/wpsoutputs SANITIZE_FILE := https://github.com/Ouranosinc/PAVICS-e2e-workflow-tests/raw/master/notebooks/docs/output-sanitize.cfg @@ -43,9 +39,9 @@ help: ## Build targets .PHONY: install -install: install-cdo venv +install: install-cdo @echo "Installing application ..." - @-bash -c '${PIP} install -e .' + @-bash -c 'poetry install' @echo "\nStart service with \`thunderbird start'" .PHONY: install-cdo @@ -57,13 +53,12 @@ install-cdo: .PHONY: install-ci install-ci: install-cdo @echo "Installing ci requirements" - @-bash -c 'pip install -r requirements.txt' - @-bash -c 'pip install -e ".[dev]"' + @-bash -c 'poetry install --with=dev' .PHONY: develop -develop: install-cdo venv +develop: install-cdo @echo "Installing development requirements for tests and docs ..." - @-bash -c '${PIP} install -e ".[dev]"' + @-bash -c 'poetry install --with=dev' # These commands have been disabled until further notice. Due to the issues with # cdo's signal handling, we cannot reliably start/stop using make. @@ -121,21 +116,17 @@ clean-dist: clean ## do not use git clean -e/--exclude here, add them to .gitignore instead @-git clean -dfx -.PHONY: venv -venv: - test -d $(VENV) || python3 -m venv $(VENV) - ## Test targets .PHONY: test -test: venv +test: @echo "Running tests (skip slow and online tests) ..." - @bash -c '${PYTHON} -m pytest -v -m "not slow and not online" tests/' + @bash -c 'poetry run pytest -v -m "not slow and not online" tests/' .PHONY: test-all -test-all: venv +test-all: @echo "Running all tests (including slow and online tests) ..." - @bash -c '${PYTHON} -m pytest -v tests/' + @bash -c 'poetry run pytest -v tests/' .PHONY: notebook-sanitizer notebook-sanitizer: @@ -145,40 +136,40 @@ notebook-sanitizer: .PHONY: test-notebooks test-notebooks: notebook-sanitizer @echo "Running notebook-based tests" - @bash -c "source $(VENV)/bin/activate && env LOCAL_URL=$(LOCAL_URL) pytest --nbval --verbose $(CURDIR)/notebooks/ --sanitize-with $(CURDIR)/docs/output-sanitize.cfg --ignore $(CURDIR)/notebooks/.ipynb_checkpoints" + @bash -c "poetry shell && env LOCAL_URL=$(LOCAL_URL) pytest --nbval --verbose $(CURDIR)/notebooks/ --sanitize-with $(CURDIR)/docs/output-sanitize.cfg --ignore $(CURDIR)/notebooks/.ipynb_checkpoints" .PHONY: test-notebooks-prod test-notebooks-prod: notebook-sanitizer @echo "Running notebook-based tests against production instance of thunderbird" - @bash -c "source $(VENV)/bin/activate && pytest --nbval --verbose $(CURDIR)/notebooks/ --sanitize-with $(CURDIR)/docs/output-sanitize.cfg --ignore $(CURDIR)/notebooks/.ipynb_checkpoints" + @bash -c "poetry shell && pytest --nbval --verbose $(CURDIR)/notebooks/ --sanitize-with $(CURDIR)/docs/output-sanitize.cfg --ignore $(CURDIR)/notebooks/.ipynb_checkpoints" .PHONY: test-notebooks-dev test-notebooks-dev: notebook-sanitizer @echo "Running notebook-based tests against development instance of thunderbird" - @bash -c "source $(VENV)/bin/activate && env DEV_URL=http://docker-dev03.pcic.uvic.ca:30099/wps pytest --nbval --verbose $(CURDIR)/notebooks/ --sanitize-with $(CURDIR)/docs/output-sanitize.cfg --ignore $(CURDIR)/notebooks/.ipynb_checkpoints" + @bash -c "poetry shell && env DEV_URL=http://marble-dev01.pcic.uvic.ca:30099/wps pytest --nbval --verbose $(CURDIR)/notebooks/ --sanitize-with $(CURDIR)/docs/output-sanitize.cfg --ignore $(CURDIR)/notebooks/.ipynb_checkpoints" .PHONY: test-notebooks-custom test-notebooks-custom: notebook-sanitizer @echo "Running notebook-based tests against custom instance of thunderbird" - @bash -c "source $(VENV)/bin/activate && env DEV_URL=http://docker-dev03.pcic.uvic.ca:$(DEV_PORT)/wps pytest --nbval --verbose $(CURDIR)/notebooks/ --sanitize-with $(CURDIR)/docs/output-sanitize.cfg --ignore $(CURDIR)/notebooks/.ipynb_checkpoints" + @bash -c "poetry shell && env DEV_URL=http://marble-dev01.pcic.uvic.ca:$(DEV_PORT)/wps pytest --nbval --verbose $(CURDIR)/notebooks/ --sanitize-with $(CURDIR)/docs/output-sanitize.cfg --ignore $(CURDIR)/notebooks/.ipynb_checkpoints" .PHONY: lint lint: venv @echo "Running black code style checks ..." - @bash -c '${PYTHON} -m black . --check' + @bash -c 'poetry run black . --check' ## Sphinx targets .PHONY: docs docs: @echo "Updating notebook docs" - @bash -c 'source $(VENV)/bin/activate && jupyter nbconvert --to html notebooks/* --output-dir docs/formatted_demos/' + @bash -c 'poetry shell && jupyter nbconvert --to html notebooks/* --output-dir docs/formatted_demos/' ## Deployment targets .PHONY: dist dist: clean @echo "Builds source and wheel package ..." - @-python3 setup.py sdist - @-python3 setup.py bdist_wheel + @bash -c 'poetry build -f sdist' + @bash -c 'poetry build -f wheel' ls -l dist From 299e1c268f064e798a1aa19e038896caef1fa2db Mon Sep 17 00:00:00 2001 From: Eric Yvorchuk Date: Fri, 24 May 2024 14:49:22 -0700 Subject: [PATCH 03/32] Update Dockerfile --- Dockerfile | 21 +++++++++++---------- 1 file changed, 11 insertions(+), 10 deletions(-) diff --git a/Dockerfile b/Dockerfile index 02f67ba..6c16756 100644 --- a/Dockerfile +++ b/Dockerfile @@ -1,25 +1,26 @@ -FROM python:3.8-slim +FROM python:3.11-slim LABEL Maintainer=https://github.com/pacificclimate/thunderbird Description="thunderbird WPS" Vendor="pcic" Version="1.2.3" ENV DEBIAN_FRONTEND=noninteractive ENV PIP_INDEX_URL="https://pypi.pacificclimate.org/simple/" COPY . /tmp +ADD poetry.lock /tmp +ADD pyproject.toml /tmp WORKDIR /tmp RUN apt-get update && \ - apt-get install -y build-essential cdo libhdf5-serial-dev netcdf-bin libnetcdf-dev && \ + apt-get install -y build-essential cdo curl libhdf5-serial-dev netcdf-bin libnetcdf-dev && \ rm -rf /var/lib/apt/lists/* && \ - # this line combats the issue found here: - # https://superuser.com/questions/1347723/arch-on-wsl-libqt5core-so-5-not-found-despite-being-installed - strip --remove-section=.note.ABI-tag /usr/lib/x86_64-linux-gnu/libQt5Core.so.5 && \ # Removing this package prevents a scan failure. It will be reintroduced # once 1.24.2 becomes available through the base image. # Issue link: https://github.com/advisories/GHSA-mh33-7rrq-662w - apt-get remove -y python3-urllib3 && \ - pip install -U pip && \ - pip install . && \ - pip install gunicorn + apt-get remove -y python3-urllib3 + +RUN curl -sSL https://install.python-poetry.org | python3 - +ENV PATH=/root/.local/bin:$PATH +RUN poetry install && \ + poetry add gunicorn EXPOSE 5000 -CMD ["gunicorn", "--bind=0.0.0.0:5000", "thunderbird.wsgi:application"] \ No newline at end of file +CMD ["poetry", "run", "gunicorn", "--bind=0.0.0.0:5000", "thunderbird.wsgi:application"] From 511014e5148f4bd59cca8fe52fee355f07bae054 Mon Sep 17 00:00:00 2001 From: Eric Yvorchuk Date: Fri, 24 May 2024 15:45:55 -0700 Subject: [PATCH 04/32] Fix Dockerfile --- Dockerfile | 17 +++++------------ 1 file changed, 5 insertions(+), 12 deletions(-) diff --git a/Dockerfile b/Dockerfile index 6c16756..1818476 100644 --- a/Dockerfile +++ b/Dockerfile @@ -1,26 +1,19 @@ -FROM python:3.11-slim +FROM python:3.10-slim LABEL Maintainer=https://github.com/pacificclimate/thunderbird Description="thunderbird WPS" Vendor="pcic" Version="1.2.3" ENV DEBIAN_FRONTEND=noninteractive ENV PIP_INDEX_URL="https://pypi.pacificclimate.org/simple/" COPY . /tmp -ADD poetry.lock /tmp -ADD pyproject.toml /tmp WORKDIR /tmp RUN apt-get update && \ - apt-get install -y build-essential cdo curl libhdf5-serial-dev netcdf-bin libnetcdf-dev && \ - rm -rf /var/lib/apt/lists/* && \ - # Removing this package prevents a scan failure. It will be reintroduced - # once 1.24.2 becomes available through the base image. - # Issue link: https://github.com/advisories/GHSA-mh33-7rrq-662w - apt-get remove -y python3-urllib3 + apt-get install -y cdo curl libhdf5-serial-dev netcdf-bin libnetcdf-dev && \ + rm -rf /var/lib/apt/lists/* RUN curl -sSL https://install.python-poetry.org | python3 - ENV PATH=/root/.local/bin:$PATH -RUN poetry install && \ - poetry add gunicorn +RUN poetry install EXPOSE 5000 -CMD ["poetry", "run", "gunicorn", "--bind=0.0.0.0:5000", "thunderbird.wsgi:application"] +CMD ["poetry", "run", "gunicorn", "-t 60", "--bind=0.0.0.0:5000", "thunderbird.wsgi:application"] From d0c14d15224af58311921d921192193052b572de Mon Sep 17 00:00:00 2001 From: Eric Yvorchuk Date: Fri, 24 May 2024 15:46:08 -0700 Subject: [PATCH 05/32] Update python-ci.yml --- .github/workflows/python-ci.yml | 10 ++++++---- 1 file changed, 6 insertions(+), 4 deletions(-) diff --git a/.github/workflows/python-ci.yml b/.github/workflows/python-ci.yml index e289baa..f4fc3ad 100644 --- a/.github/workflows/python-ci.yml +++ b/.github/workflows/python-ci.yml @@ -8,7 +8,7 @@ jobs: runs-on: ubuntu-20.04 strategy: matrix: - python-version: [3.7, 3.8] + python-version: ["3.9", "3.10", "3.11"] steps: - uses: actions/checkout@v2 @@ -18,14 +18,16 @@ jobs: python-version: ${{ matrix.python-version }} - name: Install dependencies run: | + poetry env use python${{ matrix.python-version }} make install-ci - name: Test with pytest (full) if: github.ref == 'refs/heads/master' run: | - py.test -m "not online" -v + make test-all - name: Test with pytest (fast) if: github.ref != 'refs/heads/master' run: | - py.test -m "not online and not slow" -v + make test - name: Code Quality - run: black . --check + run: | + poetry run black . --check From 3c6d3059589bc86c5a0c0041d471b39355159606 Mon Sep 17 00:00:00 2001 From: Eric Yvorchuk Date: Fri, 24 May 2024 15:48:46 -0700 Subject: [PATCH 06/32] Install poetry in CI --- .github/workflows/python-ci.yml | 4 ++++ 1 file changed, 4 insertions(+) diff --git a/.github/workflows/python-ci.yml b/.github/workflows/python-ci.yml index f4fc3ad..99243e6 100644 --- a/.github/workflows/python-ci.yml +++ b/.github/workflows/python-ci.yml @@ -16,6 +16,10 @@ jobs: uses: actions/setup-python@v2 with: python-version: ${{ matrix.python-version }} + - name: Install poetry + run: | + curl -sSL https://install.python-poetry.org | python3 - + echo "$HOME/.local/bin" >> $GITHUB_PATH - name: Install dependencies run: | poetry env use python${{ matrix.python-version }} From 4433485a9bacc799e55adc4aa45813517d5d0c67 Mon Sep 17 00:00:00 2001 From: Eric Yvorchuk Date: Mon, 27 May 2024 09:59:47 -0700 Subject: [PATCH 07/32] Update dependencies --- poetry.lock | 284 ++++++++++++++++++++++++------------------------- pyproject.toml | 7 +- 2 files changed, 143 insertions(+), 148 deletions(-) diff --git a/poetry.lock b/poetry.lock index c319f5f..abb30ed 100644 --- a/poetry.lock +++ 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description = "Backport of pathlib-compatible object wrapper for zip files" optional = false python-versions = ">=3.8" files = [ - {file = "zipp-3.18.2-py3-none-any.whl", hash = "sha256:dce197b859eb796242b0622af1b8beb0a722d52aa2f57133ead08edd5bf5374e"}, - {file = "zipp-3.18.2.tar.gz", hash = "sha256:6278d9ddbcfb1f1089a88fde84481528b07b0e10474e09dcfe53dad4069fa059"}, + {file = "zipp-3.19.0-py3-none-any.whl", hash = "sha256:96dc6ad62f1441bcaccef23b274ec471518daf4fbbc580341204936a5a3dddec"}, + {file = "zipp-3.19.0.tar.gz", hash = "sha256:952df858fb3164426c976d9338d3961e8e8b3758e2e059e0f754b8c4262625ee"}, ] [package.extras] @@ -4152,4 +4146,4 @@ testing = ["big-O", "jaraco.functools", "jaraco.itertools", "jaraco.test", "more [metadata] lock-version = "2.0" python-versions = ">=3.9,<4" -content-hash = "7dbf5aa991fb275d87ee3e0d4219941220b3b27c66b45aa6229d0e29d59d5a59" +content-hash = "c153f5d35e284d7eb6e41ea401c550d6ebb8ec85f74ee66b8497bda27601e17a" diff --git a/pyproject.toml b/pyproject.toml index d5e843f..502613f 100644 --- a/pyproject.toml +++ b/pyproject.toml @@ -45,12 +45,13 @@ priority = "supplemental" [tool.poetry.dependencies] python = ">=3.9,<4" ce-dataprep = { version = "^0.8.8", source = "pcic" } -cftime = "1.1.3" +cftime = "1.6.3" click = "^8.1.7" gunicorn = "^22.0.0" jinja2 = ">=2.11.3,<3.1.0" -netcdf4 = "1.5.8" -psutil = "5.7.0" +netcdf4 = "1.6.2" +numpy = "^1.20.0" +psutil = "5.9.8" pywps = "4.2.9" xarray = "^2024.2.0" nchelpers = { version = "^5.5.11", source = "pcic" } From 63bc25f68f7d8a5c15b0d5b1524aaf8f886f1a2f Mon Sep 17 00:00:00 2001 From: Eric Yvorchuk Date: Mon, 27 May 2024 10:02:42 -0700 Subject: [PATCH 08/32] Format with black --- tests/test_wps_decompose_flow_vectors.py | 105 +++++++++++++++--- tests/test_wps_generate_climos.py | 27 ++++- tests/test_wps_generate_prsn.py | 45 ++++++-- tests/test_wps_split_merged_climos.py | 6 +- tests/test_wps_update_metadata.py | 24 ++-- thunderbird/cli.py | 5 +- .../processes/wps_decompose_flow_vectors.py | 6 +- thunderbird/processes/wps_update_metadata.py | 7 +- thunderbird/utils.py | 3 +- 9 files changed, 182 insertions(+), 46 deletions(-) diff --git a/tests/test_wps_decompose_flow_vectors.py b/tests/test_wps_decompose_flow_vectors.py index 14f3599..542e9e9 100644 --- a/tests/test_wps_decompose_flow_vectors.py +++ b/tests/test_wps_decompose_flow_vectors.py @@ -34,10 +34,19 @@ def build_params(netcdf, kwargs): @pytest.mark.slow @pytest.mark.online @pytest.mark.parametrize( - ("opendap"), flow_vectors_opendap, + ("opendap"), + flow_vectors_opendap, ) @pytest.mark.parametrize( - ("kwargs"), [({"dest_file": "output.nc", "variable": "Flow_Direction",}),], + ("kwargs"), + [ + ( + { + "dest_file": "output.nc", + "variable": "Flow_Direction", + } + ), + ], ) def test_wps_decompose_flow_vectors_opendap(opendap, kwargs): params = build_params(opendap, kwargs) @@ -45,10 +54,19 @@ def test_wps_decompose_flow_vectors_opendap(opendap, kwargs): @pytest.mark.parametrize( - ("netcdf"), flow_vectors_nc, + ("netcdf"), + flow_vectors_nc, ) @pytest.mark.parametrize( - ("kwargs"), [({"dest_file": "output.nc", "variable": "Flow_Direction",}),], + ("kwargs"), + [ + ( + { + "dest_file": "output.nc", + "variable": "Flow_Direction", + } + ), + ], ) def test_wps_decompose_flow_vectors_netcdf(netcdf, kwargs): params = build_params(netcdf, kwargs) @@ -56,10 +74,19 @@ def test_wps_decompose_flow_vectors_netcdf(netcdf, kwargs): @pytest.mark.parametrize( - ("netcdf"), non_flow_vectors_nc, + ("netcdf"), + non_flow_vectors_nc, ) @pytest.mark.parametrize( - ("kwargs"), [({"dest_file": "output.nc", "variable": "Flow_Direction",}),], + ("kwargs"), + [ + ( + { + "dest_file": "output.nc", + "variable": "Flow_Direction", + } + ), + ], ) def test_source_check(netcdf, kwargs): params = build_params(netcdf, kwargs) @@ -67,20 +94,66 @@ def test_source_check(netcdf, kwargs): @pytest.mark.parametrize( - ("netcdf"), flow_vectors_nc, + ("netcdf"), + flow_vectors_nc, ) @pytest.mark.parametrize( ("kwargs"), [ - ({"dest_file": "output.nc", "variable": "not a variable",}), - ({"dest_file": "output.nc", "variable": "crs",}), - ({"dest_file": "output.nc", "variable": "lat",}), - ({"dest_file": "output.nc", "variable": "lon",}), - ({"dest_file": "output.nc", "variable": "diffusion",}), - ({"dest_file": "output.nc", "variable": "Flow_Distance",}), - ({"dest_file": "output.nc", "variable": "Basin_ID",}), - ({"dest_file": "output.nc", "variable": "velocity",}), - ({"dest_file": "output.nc", "variable": "flow_direction",}), + ( + { + "dest_file": "output.nc", + "variable": "not a variable", + } + ), + ( + { + "dest_file": "output.nc", + "variable": "crs", + } + ), + ( + { + "dest_file": "output.nc", + "variable": "lat", + } + ), + ( + { + "dest_file": "output.nc", + "variable": "lon", + } + ), + ( + { + "dest_file": "output.nc", + "variable": "diffusion", + } + ), + ( + { + "dest_file": "output.nc", + "variable": "Flow_Distance", + } + ), + ( + { + "dest_file": "output.nc", + "variable": "Basin_ID", + } + ), + ( + { + "dest_file": "output.nc", + "variable": "velocity", + } + ), + ( + { + "dest_file": "output.nc", + "variable": "flow_direction", + } + ), ], ) def test_variable_check(netcdf, kwargs): diff --git a/tests/test_wps_generate_climos.py b/tests/test_wps_generate_climos.py index ff86cff..66c1c8e 100644 --- a/tests/test_wps_generate_climos.py +++ b/tests/test_wps_generate_climos.py @@ -64,7 +64,8 @@ def build_params(netcdf, kwargs): @pytest.mark.slow @pytest.mark.online @pytest.mark.parametrize( - ("netcdf"), opendap_data, + ("netcdf"), + opendap_data, ) @pytest.mark.parametrize( ("kwargs"), @@ -101,7 +102,8 @@ def test_wps_gen_climos_opendap_single(netcdf, kwargs): @pytest.mark.slow @pytest.mark.online @pytest.mark.parametrize( - ("netcdf"), [opendap_data], + ("netcdf"), + [opendap_data], ) @pytest.mark.parametrize( ("kwargs"), @@ -126,7 +128,10 @@ def test_wps_gen_climos_opendap_multiple(netcdf, kwargs): @pytest.mark.parametrize( ("netcdf"), - [(local_path("tiny_gcm_360_day_cal.nc")), (local_path("tiny_hydromodel_gcm.nc")),], + [ + (local_path("tiny_gcm_360_day_cal.nc")), + (local_path("tiny_hydromodel_gcm.nc")), + ], ) @pytest.mark.parametrize( ("kwargs"), @@ -151,7 +156,8 @@ def test_wps_gen_climos_input_check(netcdf, kwargs): @pytest.mark.slow @pytest.mark.parametrize( - ("netcdf"), local_test_data, + ("netcdf"), + local_test_data, ) @pytest.mark.parametrize( ("kwargs"), @@ -187,10 +193,19 @@ def test_wps_gen_climos_local_nc(netcdf, kwargs): @pytest.mark.slow @pytest.mark.parametrize( - ("netcdf"), local_test_data, + ("netcdf"), + local_test_data, ) @pytest.mark.parametrize( - ("kwargs"), [({"operation": "mean", "dry_run": "False",}),], + ("kwargs"), + [ + ( + { + "operation": "mean", + "dry_run": "False", + } + ), + ], ) def test_missing_arguments(netcdf, kwargs): params = ( diff --git a/tests/test_wps_generate_prsn.py b/tests/test_wps_generate_prsn.py index 817546d..6b5ddc4 100644 --- a/tests/test_wps_generate_prsn.py +++ b/tests/test_wps_generate_prsn.py @@ -42,10 +42,15 @@ def build_params(netcdfs, dry_run, chunk_size=None, output_file=None): @pytest.mark.parametrize( - ("netcdfs"), [local_nc_inputs, local_tiny_nc_inputs,], + ("netcdfs"), + [ + local_nc_inputs, + local_tiny_nc_inputs, + ], ) @pytest.mark.parametrize( - ("dry_run"), [("False")], + ("dry_run"), + [("False")], ) def test_default_local(netcdfs, dry_run): params = build_params(netcdfs, dry_run) @@ -53,10 +58,17 @@ def test_default_local(netcdfs, dry_run): @pytest.mark.parametrize( - ("netcdfs"), [local_nc_inputs, local_tiny_nc_inputs,], + ("netcdfs"), + [ + local_nc_inputs, + local_tiny_nc_inputs, + ], ) @pytest.mark.parametrize( - ("chunk_size", "dry_run", "output_file"), [("50", "True", "prsn_test_local.nc"),], + ("chunk_size", "dry_run", "output_file"), + [ + ("50", "True", "prsn_test_local.nc"), + ], ) def test_run_local(netcdfs, chunk_size, dry_run, output_file): params = build_params(netcdfs, dry_run, chunk_size, output_file) @@ -66,10 +78,12 @@ def test_run_local(netcdfs, chunk_size, dry_run, output_file): @pytest.mark.slow @pytest.mark.online @pytest.mark.parametrize( - ("opendaps"), [opendap_inputs], + ("opendaps"), + [opendap_inputs], ) @pytest.mark.parametrize( - ("dry_run"), [("False")], + ("dry_run"), + [("False")], ) def test_default_opendap(opendaps, dry_run): params = build_params(opendaps, dry_run) @@ -79,11 +93,14 @@ def test_default_opendap(opendaps, dry_run): @pytest.mark.slow @pytest.mark.online @pytest.mark.parametrize( - ("opendaps"), [opendap_inputs], + ("opendaps"), + [opendap_inputs], ) @pytest.mark.parametrize( ("chunk_size", "dry_run", "output_file"), - [("50", "False", "prsn_test_opendap.nc"),], + [ + ("50", "False", "prsn_test_opendap.nc"), + ], ) def test_run_opendap(opendaps, chunk_size, dry_run, output_file): params = build_params(opendaps, dry_run, chunk_size, output_file) @@ -115,8 +132,16 @@ def test_run_opendap(opendaps, chunk_size, dry_run, output_file): @pytest.mark.parametrize( ("chunk_size", "dry_run", "output_file"), [ - ("100", "True", "prsn_test_mixed1.nc",), - ("100", "False", "prsn_test_mixed2.nc",), + ( + "100", + "True", + "prsn_test_mixed1.nc", + ), + ( + "100", + "False", + "prsn_test_mixed2.nc", + ), ], ) def test_run_mixed(netcdfs, chunk_size, dry_run, output_file): diff --git a/tests/test_wps_split_merged_climos.py b/tests/test_wps_split_merged_climos.py index d8e23ba..d0c75c1 100644 --- a/tests/test_wps_split_merged_climos.py +++ b/tests/test_wps_split_merged_climos.py @@ -29,7 +29,8 @@ def run_multiple_files(netcdfs): @pytest.mark.parametrize( - "netcdf", climo_local_files, + "netcdf", + climo_local_files, ) def test_single_file_local(netcdf): run_single_file(netcdf) @@ -48,7 +49,8 @@ def test_multiple_files_local(netcdfs): @pytest.mark.online @pytest.mark.parametrize( - "netcdf", climo_opendaps, + "netcdf", + climo_opendaps, ) def test_single_file_opendap(netcdf): run_single_file(netcdf) diff --git a/tests/test_wps_update_metadata.py b/tests/test_wps_update_metadata.py index b41a6a0..f64a0f1 100644 --- a/tests/test_wps_update_metadata.py +++ b/tests/test_wps_update_metadata.py @@ -39,10 +39,12 @@ def build_params(netcdf, updates): @pytest.mark.online @pytest.mark.parametrize( - ("netcdf"), opendap_data, + ("netcdf"), + opendap_data, ) @pytest.mark.parametrize( - ("updates"), updates_yaml, + ("updates"), + updates_yaml, ) def test_wps_update_metadata_opendap_yaml(netcdf, updates): run_wps_process(UpdateMetadata(), build_params(netcdf, updates)) @@ -50,30 +52,36 @@ def test_wps_update_metadata_opendap_yaml(netcdf, updates): @pytest.mark.online @pytest.mark.parametrize( - ("netcdf"), opendap_data, + ("netcdf"), + opendap_data, ) @pytest.mark.parametrize( - ("updates"), updates_str, + ("updates"), + updates_str, ) def test_wps_update_metadata_opendap_str(netcdf, updates): run_wps_process(UpdateMetadata(), build_params(netcdf, updates)) @pytest.mark.parametrize( - ("netcdf"), local_data, + ("netcdf"), + local_data, ) @pytest.mark.parametrize( - ("updates"), updates_yaml, + ("updates"), + updates_yaml, ) def test_wps_update_metadata_netcdf_yaml(netcdf, updates): run_wps_process(UpdateMetadata(), build_params(netcdf, updates)) @pytest.mark.parametrize( - ("netcdf"), local_data, + ("netcdf"), + local_data, ) @pytest.mark.parametrize( - ("updates"), updates_str, + ("updates"), + updates_str, ) def test_wps_update_metadata_netcdf_str(netcdf, updates): run_wps_process(UpdateMetadata(), build_params(netcdf, updates)) diff --git a/thunderbird/cli.py b/thunderbird/cli.py index 59aeae2..ab856d5 100644 --- a/thunderbird/cli.py +++ b/thunderbird/cli.py @@ -138,7 +138,10 @@ def stop(): help="hostname in PyWPS configuration.", ) @click.option( - "--port", metavar="PORT", default="5000", help="port in PyWPS configuration.", + "--port", + metavar="PORT", + default="5000", + help="port in PyWPS configuration.", ) @click.option( "--maxsingleinputsize", diff --git a/thunderbird/processes/wps_decompose_flow_vectors.py b/thunderbird/processes/wps_decompose_flow_vectors.py index 1e93fff..31af95f 100644 --- a/thunderbird/processes/wps_decompose_flow_vectors.py +++ b/thunderbird/processes/wps_decompose_flow_vectors.py @@ -47,7 +47,11 @@ def __init__(self): "netCDF variable describing flow direction", data_type="string", ), - LiteralInput("dest_file", "destination netCDF file", data_type="string",), + LiteralInput( + "dest_file", + "destination netCDF file", + data_type="string", + ), log_level, ] outputs = [ diff --git a/thunderbird/processes/wps_update_metadata.py b/thunderbird/processes/wps_update_metadata.py index 249cd4d..422a378 100644 --- a/thunderbird/processes/wps_update_metadata.py +++ b/thunderbird/processes/wps_update_metadata.py @@ -40,7 +40,12 @@ def __init__(self): abstract="The filepath of an updates file that specifies what to do to the metadata it finds in the NetCDF file", min_occurs=0, max_occurs=1, - supported_formats=[Format(mime_type="text/x-yaml", extension=".yaml",)], + supported_formats=[ + Format( + mime_type="text/x-yaml", + extension=".yaml", + ) + ], ), LiteralInput( "updates_string", diff --git a/thunderbird/utils.py b/thunderbird/utils.py index d9154c7..96f4641 100644 --- a/thunderbird/utils.py +++ b/thunderbird/utils.py @@ -36,7 +36,8 @@ def dry_run_info(filename, dry_run_method, **kwargs): def dry_output_filename(outdir, filename): if filename.endswith(".nc"): return os.path.join( - outdir, os.path.basename(filename).split(".")[0] + "_dry.txt", + outdir, + os.path.basename(filename).split(".")[0] + "_dry.txt", ) else: return os.path.join(outdir, filename) From 0e77a823966c226984b84aa477475295f441d4c5 Mon Sep 17 00:00:00 2001 From: Eric Yvorchuk Date: Mon, 27 May 2024 10:16:03 -0700 Subject: [PATCH 09/32] Add .ncrc to fix SSL error when making OPeNDAP requests --- .ncrc | 1 + 1 file changed, 1 insertion(+) create mode 100644 .ncrc diff --git a/.ncrc b/.ncrc new file mode 100644 index 0000000..538ddc2 --- /dev/null +++ b/.ncrc @@ -0,0 +1 @@ +HTTP.SSL.CAINFO=/etc/ssl/certs/ca-certificates.crt From 8dc4a88d994b5f315b41c2da701d56ba5462af3b Mon Sep 17 00:00:00 2001 From: Eric Yvorchuk Date: Mon, 27 May 2024 13:22:22 -0700 Subject: [PATCH 10/32] Change default thunderbird host --- thunderbird/utils.py | 2 +- 1 file changed, 1 insertion(+), 1 deletion(-) diff --git a/thunderbird/utils.py b/thunderbird/utils.py index 96f4641..f2a08e7 100644 --- a/thunderbird/utils.py +++ b/thunderbird/utils.py @@ -53,4 +53,4 @@ def get_url(): if url: return url - return "https://docker-dev03.pcic.uvic.ca/twitcher/ows/proxy/thunderbird/wps" + return "https://marble-dev01.pcic.uvic.ca/twitcher/ows/proxy/thunderbird/wps" From de53577fabb421b3dcfec097084b3699af453e19 Mon Sep 17 00:00:00 2001 From: Eric Yvorchuk Date: Mon, 27 May 2024 13:23:06 -0700 Subject: [PATCH 11/32] Get thredds host from environment --- .env | 1 + poetry.lock | 650 ++++++++++++++++++++++++++++++++++++++++++++----- pyproject.toml | 1 + 3 files changed, 593 insertions(+), 59 deletions(-) create mode 100644 .env diff --git a/.env b/.env new file mode 100644 index 0000000..34fc6f3 --- /dev/null +++ b/.env @@ -0,0 +1 @@ +THREDDS_HOST="marble-dev01.pcic.uvic.ca" diff --git a/poetry.lock b/poetry.lock index abb30ed..8531239 100644 --- a/poetry.lock +++ b/poetry.lock @@ -181,21 +181,6 @@ files = [ [package.extras] dev = ["freezegun (>=1.0,<2.0)", "pytest (>=6.0)", "pytest-cov"] -[[package]] -name = "backports-tarfile" -version = "1.1.1" -description = "Backport of CPython tarfile module" -optional = false -python-versions = ">=3.8" -files = [ - {file = "backports.tarfile-1.1.1-py3-none-any.whl", hash = "sha256:73e0179647803d3726d82e76089d01d8549ceca9bace469953fcb4d97cf2d417"}, - {file = "backports_tarfile-1.1.1.tar.gz", hash = "sha256:9c2ef9696cb73374f7164e17fc761389393ca76777036f5aad42e8b93fcd8009"}, -] - -[package.extras] -docs = ["furo", "jaraco.packaging (>=9.3)", "rst.linker (>=1.9)", "sphinx (>=3.5)", "sphinx-lint"] -testing = ["jaraco.test", "pytest (>=6,!=8.1.*)", "pytest-checkdocs (>=2.4)", "pytest-cov", "pytest-enabler (>=2.2)"] - [[package]] name = "beautifulsoup4" version = "4.9.3" @@ -330,6 +315,31 @@ files = [ {file = "boltons-24.0.0.tar.gz", hash = "sha256:7153feccaea1ff2e1472f68d4b57fadb796a2ee49d29f638f1c9cd8fb5ebd916"}, ] +[[package]] +name = "build" +version = "1.2.1" +description = "A simple, correct Python build frontend" +optional = false +python-versions = ">=3.8" +files = [ + {file = "build-1.2.1-py3-none-any.whl", hash = "sha256:75e10f767a433d9a86e50d83f418e83efc18ede923ee5ff7df93b6cb0306c5d4"}, + {file = "build-1.2.1.tar.gz", hash = "sha256:526263f4870c26f26c433545579475377b2b7588b6f1eac76a001e873ae3e19d"}, +] + +[package.dependencies] +colorama = {version = "*", markers = "os_name == \"nt\""} +importlib-metadata = {version = ">=4.6", markers = "python_full_version < \"3.10.2\""} +packaging = ">=19.1" +pyproject_hooks = "*" +tomli = {version = ">=1.1.0", markers = "python_version < \"3.11\""} + +[package.extras] +docs = ["furo (>=2023.08.17)", "sphinx (>=7.0,<8.0)", "sphinx-argparse-cli (>=1.5)", "sphinx-autodoc-typehints (>=1.10)", "sphinx-issues (>=3.0.0)"] +test = ["build[uv,virtualenv]", "filelock (>=3)", "pytest (>=6.2.4)", "pytest-cov (>=2.12)", "pytest-mock (>=2)", "pytest-rerunfailures (>=9.1)", "pytest-xdist (>=1.34)", "setuptools (>=42.0.0)", "setuptools (>=56.0.0)", "setuptools (>=56.0.0)", "setuptools (>=67.8.0)", "wheel (>=0.36.0)"] +typing = ["build[uv]", "importlib-metadata (>=5.1)", "mypy (>=1.9.0,<1.10.0)", "tomli", "typing-extensions (>=3.7.4.3)"] +uv = ["uv (>=0.1.18)"] +virtualenv = ["virtualenv (>=20.0.35)"] + [[package]] name = "bump2version" version = "1.0.1" @@ -355,6 +365,27 @@ files = [ [package.dependencies] bump2version = "*" +[[package]] +name = "cachecontrol" +version = "0.14.0" +description = "httplib2 caching for requests" +optional = false 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a/pyproject.toml b/pyproject.toml index 502613f..eb3a442 100644 --- a/pyproject.toml +++ b/pyproject.toml @@ -58,6 +58,7 @@ nchelpers = { version = "^5.5.11", source = "pcic" } werkzeug = "1.0.1" wps-tools = { version = "^2.1.1", source = "pcic" } cdo = "1.6.0" +poetry-dotenv-plugin = "^0.2.0" [tool.poetry.group.dev.dependencies] pytest = ">=6.0" From f2bf96fca6016fb6a895a5b2a9509d41e0f4b9fb Mon Sep 17 00:00:00 2001 From: Eric Yvorchuk Date: Mon, 27 May 2024 13:23:37 -0700 Subject: [PATCH 12/32] Update local thunderbird URL --- Makefile | 2 +- 1 file changed, 1 insertion(+), 1 deletion(-) diff --git a/Makefile b/Makefile index cdc0e8e..170b9c6 100644 --- a/Makefile +++ b/Makefile @@ -3,7 +3,7 @@ APP_ROOT := $(abspath $(lastword $(MAKEFILE_LIST))/..) APP_NAME := thunderbird # Notebook targets -LOCAL_URL = http://localhost:5000 +LOCAL_URL = http://localhost:5000/wps DEV_PORT ?= $(shell bash -c 'read -ep "Target port: " port; echo $$port') # Used in target refresh-notebooks to make it looks like the notebooks have From 109b514d24c7f952e586765aba007f0f06b27e51 Mon Sep 17 00:00:00 2001 From: Eric Yvorchuk Date: Mon, 27 May 2024 13:24:45 -0700 Subject: [PATCH 13/32] Update notebooks and formatted demos --- .../wps_decompose_flow_vectors_demo.html | 16831 +++++---------- .../wps_generate_climos_demo.html | 16959 +++++----------- .../wps_generate_prsn_demo.html | 16869 +++++---------- .../wps_split_merged_climos_demo.html | 16556 +++++---------- .../wps_update_metadata_demo.html | 16910 +++++---------- .../wps_decompose_flow_vectors_demo.ipynb | 17 +- notebooks/wps_generate_climos_demo.ipynb | 22 +- notebooks/wps_generate_prsn_demo.ipynb | 34 +- notebooks/wps_split_merged_climos_demo.ipynb | 23 +- notebooks/wps_update_metadata_demo.ipynb | 45 +- 10 files changed, 25122 insertions(+), 59144 deletions(-) diff --git a/docs/formatted_demos/wps_decompose_flow_vectors_demo.html b/docs/formatted_demos/wps_decompose_flow_vectors_demo.html index 991fb74..704afea 100644 --- a/docs/formatted_demos/wps_decompose_flow_vectors_demo.html +++ b/docs/formatted_demos/wps_decompose_flow_vectors_demo.html @@ -1,18 +1,14 @@ - - - + + + wps_decompose_flow_vectors_demo - - - - - - - - - - +.jp-OutputArea-output pre { + line-height: inherit; + font-family: inherit; +} + +.jp-RenderedText pre { + color: var(--jp-content-font-color1); + font-size: var(--jp-code-font-size); +} +/* Hiding the collapser by default */ +.jp-Collapser { + display: none; +} + +@page { + margin: 0.5in; /* Margin for each printed piece of paper */ +} +@media print { + .jp-Cell-inputWrapper, + .jp-Cell-outputWrapper { + display: block; + } +} + - - - + + - - + + + + +
+
- - - - - - - diff --git a/docs/formatted_demos/wps_generate_climos_demo.html b/docs/formatted_demos/wps_generate_climos_demo.html index d7379c3..2a23487 100644 --- a/docs/formatted_demos/wps_generate_climos_demo.html +++ b/docs/formatted_demos/wps_generate_climos_demo.html @@ -1,18 +1,14 @@ - - - + + + wps_generate_climos_demo - - - - - - - +.jp-Cell-Placeholder { + padding-left: 55px; +} + +.jp-Cell-Placeholder-wrapper { + background: #fff; + border: 1px solid; + border-color: #e5e6e9 #dfe0e4 #d0d1d5; + border-radius: 4px; + -webkit-border-radius: 4px; + margin: 10px 15px; +} + +.jp-Cell-Placeholder-wrapper-inner { + padding: 15px; + position: relative; +} + +.jp-Cell-Placeholder-wrapper-body { + background-repeat: repeat; + background-size: 50% auto; +} + +.jp-Cell-Placeholder-wrapper-body div { + background: #f6f7f8; + background-image: -webkit-linear-gradient( + left, + #f6f7f8 0%, + #edeef1 20%, + #f6f7f8 40%, + #f6f7f8 100% + ); + background-repeat: no-repeat; + background-size: 800px 104px; + height: 104px; + position: absolute; + right: 15px; + left: 15px; + top: 15px; +} - + - +/* Hiding the collapser by default */ +.jp-Collapser { + display: none; +} +@page { + margin: 0.5in; /* Margin for each printed piece of paper */ +} +@media print { + .jp-Cell-inputWrapper, + .jp-Cell-outputWrapper { + display: block; + } +} + - - - + + - - + + + + +
+
- - - - - - - diff --git a/docs/formatted_demos/wps_generate_prsn_demo.html b/docs/formatted_demos/wps_generate_prsn_demo.html index 218c7a4..e3b5e1e 100644 --- a/docs/formatted_demos/wps_generate_prsn_demo.html +++ b/docs/formatted_demos/wps_generate_prsn_demo.html @@ -1,18 +1,14 @@ - - - + + + wps_generate_prsn_demo - - - - - - - - - - +/* Hiding the collapser by default */ +.jp-Collapser { + display: none; +} +@page { + margin: 0.5in; /* Margin for each printed piece of paper */ +} +@media print { + .jp-Cell-inputWrapper, + .jp-Cell-outputWrapper { + display: block; + } +} + - - - + + - - + + + + +
+
- - - - - - - diff --git a/docs/formatted_demos/wps_split_merged_climos_demo.html b/docs/formatted_demos/wps_split_merged_climos_demo.html index 51df62e..9d88fc5 100644 --- a/docs/formatted_demos/wps_split_merged_climos_demo.html +++ b/docs/formatted_demos/wps_split_merged_climos_demo.html @@ -1,18 +1,14 @@ - - - + + + wps_split_merged_climos_demo - - - - - - - +.jp-Cell-Placeholder { + padding-left: 55px; +} + +.jp-Cell-Placeholder-wrapper { + background: #fff; + border: 1px solid; + border-color: #e5e6e9 #dfe0e4 #d0d1d5; + border-radius: 4px; + -webkit-border-radius: 4px; + margin: 10px 15px; +} - + - +.jp-RenderedText pre { + color: var(--jp-content-font-color1); + font-size: var(--jp-code-font-size); +} + +/* Hiding the collapser by default */ +.jp-Collapser { + display: none; +} +@page { + margin: 0.5in; /* Margin for each printed piece of paper */ +} +@media print { + .jp-Cell-inputWrapper, + .jp-Cell-outputWrapper { + display: block; + } +} + - - - + + - - + + + + +
+
- - - - - - - diff --git a/docs/formatted_demos/wps_update_metadata_demo.html b/docs/formatted_demos/wps_update_metadata_demo.html index 81b3c07..956f872 100644 --- a/docs/formatted_demos/wps_update_metadata_demo.html +++ b/docs/formatted_demos/wps_update_metadata_demo.html @@ -1,18 +1,14 @@ - - - + + + wps_update_metadata_demo - - - - - - - - - - +.jp-OutputArea-output pre { + line-height: inherit; + font-family: inherit; +} + +.jp-RenderedText pre { + color: var(--jp-content-font-color1); + font-size: var(--jp-code-font-size); +} +/* Hiding the collapser by default */ +.jp-Collapser { + display: none; +} + +@page { + margin: 0.5in; /* Margin for each printed piece of paper */ +} +@media print { + .jp-Cell-inputWrapper, + .jp-Cell-outputWrapper { + display: block; + } +} + - - - + + - - + + + + +
+
- - - - - - - diff --git a/notebooks/wps_decompose_flow_vectors_demo.ipynb b/notebooks/wps_decompose_flow_vectors_demo.ipynb index 9f982db..54ef8df 100644 --- a/notebooks/wps_decompose_flow_vectors_demo.ipynb +++ b/notebooks/wps_decompose_flow_vectors_demo.ipynb @@ -34,7 +34,7 @@ "name": "stdout", "output_type": "stream", "text": [ - "Using thunderbird on https://docker-dev03.pcic.uvic.ca/twitcher/ows/proxy/thunderbird/wps\n" + "Using thunderbird on https://marble-dev01.pcic.uvic.ca/twitcher/ows/proxy/thunderbird/wps\n" ] } ], @@ -93,8 +93,8 @@ "-------\n", "output : ComplexData:mimetype:`application/x-netcdf`\n", " output netCDF file\n", - "\u001b[0;31mFile:\u001b[0m ~/code/birds/thunderbird/\n", - "\u001b[0;31mType:\u001b[0m method\n" + "\u001b[0;31mFile:\u001b[0m ~/code/thunderbird/\n", + "\u001b[0;31mType:\u001b[0m method" ] }, "metadata": {}, @@ -119,7 +119,8 @@ "metadata": {}, "outputs": [], "source": [ - "flow_vectors_file = \"https://docker-dev03.pcic.uvic.ca/twitcher/ows/proxy/thredds/dodsC/datasets/storage/data/projects/comp_support/daccs/test-data/sample_flow_parameters.nc\"\n", + "thredds_host = os.getenv(\"THREDDS_HOST\", \"marble-dev01.pcic.uvic.ca\")\n", + "flow_vectors_file = f\"https://{thredds_host}/twitcher/ows/proxy/thredds/dodsC/datasets/storage/data/projects/comp_support/daccs/test-data/sample_flow_parameters.nc\"\n", "variable = \"Flow_Direction\"\n", "dest_file = \"output.nc\"\n", "output = thunderbird.decompose_flow_vectors(netcdf=flow_vectors_file, variable=variable, dest_file=dest_file)\n", @@ -161,7 +162,7 @@ }, { "cell_type": "code", - "execution_count": 8, + "execution_count": 7, "metadata": {}, "outputs": [], "source": [ @@ -173,7 +174,7 @@ }, { "cell_type": "code", - "execution_count": 9, + "execution_count": 8, "metadata": {}, "outputs": [], "source": [ @@ -193,7 +194,7 @@ ], "metadata": { "kernelspec": { - "display_name": "Python 3", + "display_name": "Python 3 (ipykernel)", "language": "python", "name": "python3" }, @@ -207,7 +208,7 @@ "name": "python", "nbconvert_exporter": "python", "pygments_lexer": "ipython3", - "version": "3.8.5" + "version": "3.10.12" } }, "nbformat": 4, diff --git a/notebooks/wps_generate_climos_demo.ipynb b/notebooks/wps_generate_climos_demo.ipynb index 4dc8f99..567dfe8 100644 --- a/notebooks/wps_generate_climos_demo.ipynb +++ b/notebooks/wps_generate_climos_demo.ipynb @@ -22,6 +22,7 @@ "source": [ "from birdy import WPSClient\n", "from netCDF4 import Dataset\n", + "import os\n", "import re\n", "from wps_tools.testing import get_target_url\n", "from wps_tools.output_handling import auto_construct_outputs, txt_to_string, get_metalink_content, nc_to_dataset" @@ -36,7 +37,7 @@ "name": "stdout", "output_type": "stream", "text": [ - "Using thunderbird on https://docker-dev03.pcic.uvic.ca/twitcher/ows/proxy/thunderbird/wps\n" + "Using thunderbird on https://marble-dev01.pcic.uvic.ca/twitcher/ows/proxy/thunderbird/wps\n" ] } ], @@ -105,8 +106,8 @@ " Metalink object between output files\n", "dry_output : ComplexData:mimetype:`application/metalink+xml; version=4.0`\n", " Metalink object between dry output files\n", - "\u001b[0;31mFile:\u001b[0m ~/code/birds/thunderbird/notebooks/\n", - "\u001b[0;31mType:\u001b[0m method\n" + "\u001b[0;31mFile:\u001b[0m ~/code/thunderbird/notebooks/\n", + "\u001b[0;31mType:\u001b[0m method" ] }, "metadata": {}, @@ -134,8 +135,9 @@ "outputs": [], "source": [ "# Set up variables for thunderbird.generate_climos\n", - "seasonal_opendap = 'https://docker-dev03.pcic.uvic.ca/twitcher/ows/proxy/thredds/dodsC/datasets/storage/data/projects/comp_support/daccs/test-data/fdd_seasonal_CanESM2_rcp85_r1i1p1_1951-2100.nc'\n", - "annual_opendap = 'https://docker-dev03.pcic.uvic.ca/twitcher/ows/proxy/thredds/dodsC/datasets/storage/data/projects/comp_support/daccs/test-data/gdd_annual_CanESM2_rcp85_r1i1p1_1951-2100.nc'\n", + "thredds_host = os.getenv(\"THREDDS_HOST\", \"marble-dev01.pcic.uvic.ca\")\n", + "seasonal_opendap = f'https://{thredds_host}/twitcher/ows/proxy/thredds/dodsC/datasets/storage/data/projects/comp_support/daccs/test-data/fdd_seasonal_CanESM2_rcp85_r1i1p1_1951-2100.nc'\n", + "annual_opendap = f'https://{thredds_host}/twitcher/ows/proxy/thredds/dodsC/datasets/storage/data/projects/comp_support/daccs/test-data/gdd_annual_CanESM2_rcp85_r1i1p1_1951-2100.nc'\n", "operation = 'mean'\n", "climo = '6190'\n", "resolutions = 'yearly'\n", @@ -166,7 +168,7 @@ { "data": { "text/plain": [ - "[\"Dry Run\\ngenerate_climos:\\nINFO:dp.generate_climos:Processing: https://docker-dev03.pcic.uvic.ca/twitcher/ows/proxy/thredds/dodsC/datasets/storage/data/projects/comp_support/daccs/test-data/fdd_seasonal_CanESM2_rcp85_r1i1p1_1951-2100.nc\\nINFO:dp.generate_climos:climo_periods: {'6190'}\\nINFO:dp.generate_climos:project: CMIP5\\nINFO:dp.generate_climos:institution: PCIC\\nINFO:dp.generate_climos:model: CanESM2\\nINFO:dp.generate_climos:emissions: historical, rcp85\\nINFO:dp.generate_climos:run: r1i1p1\\nINFO:dp.generate_climos:dependent_varnames: ['fdd']\\nINFO:dp.generate_climos:time_resolution: seasonal\\nINFO:dp.generate_climos:is_multi_year_mean: False\\n\"]" + "[\"Dry Run\\ngenerate_climos:\\nINFO:dp.generate_climos:Processing: https://marble-dev01.pcic.uvic.ca/twitcher/ows/proxy/thredds/dodsC/datasets/storage/data/projects/comp_support/daccs/test-data/fdd_seasonal_CanESM2_rcp85_r1i1p1_1951-2100.nc\\nINFO:dp.generate_climos:climo_periods: {'6190'}\\nINFO:dp.generate_climos:project: CMIP5\\nINFO:dp.generate_climos:institution: PCIC\\nINFO:dp.generate_climos:model: CanESM2\\nINFO:dp.generate_climos:emissions: historical, rcp85\\nINFO:dp.generate_climos:run: r1i1p1\\nINFO:dp.generate_climos:dependent_varnames: ['fdd']\\nINFO:dp.generate_climos:time_resolution: seasonal\\nINFO:dp.generate_climos:is_multi_year_mean: False\\n\"]" ] }, "execution_count": 6, @@ -188,10 +190,10 @@ "name": "stdout", "output_type": "stream", "text": [ - "['http://localhost:5000/outputs/18ea7027-7ae5-11eb-82d4-85fba3d3ed5b/fdd_seasonal_CanESM2_rcp85_r1i1p1_1951-2100_dry.txt']\n", + "['https://marble-dev01.pcic.uvic.ca/wpsoutputs/11cdc88a-1c66-11ef-8399-0242ac120003/fdd_seasonal_CanESM2_rcp85_r1i1p1_1951-2100_dry.txt']\n", "Dry Run\n", "generate_climos:\n", - "INFO:dp.generate_climos:Processing: https://docker-dev03.pcic.uvic.ca/twitcher/ows/proxy/thredds/dodsC/datasets/storage/data/projects/comp_support/daccs/test-data/fdd_seasonal_CanESM2_rcp85_r1i1p1_1951-2100.nc\n", + "INFO:dp.generate_climos:Processing: https://marble-dev01.pcic.uvic.ca/twitcher/ows/proxy/thredds/dodsC/datasets/storage/data/projects/comp_support/daccs/test-data/fdd_seasonal_CanESM2_rcp85_r1i1p1_1951-2100.nc\n", "INFO:dp.generate_climos:climo_periods: {'6190'}\n", "INFO:dp.generate_climos:project: CMIP5\n", "INFO:dp.generate_climos:institution: PCIC\n", @@ -352,7 +354,7 @@ ], "metadata": { "kernelspec": { - "display_name": "Python 3", + "display_name": "Python 3 (ipykernel)", "language": "python", "name": "python3" }, @@ -366,7 +368,7 @@ "name": "python", "nbconvert_exporter": "python", "pygments_lexer": "ipython3", - "version": "3.8.5" + "version": "3.10.12" } }, "nbformat": 4, diff --git a/notebooks/wps_generate_prsn_demo.ipynb b/notebooks/wps_generate_prsn_demo.ipynb index 59ad2df..e69d38b 100644 --- a/notebooks/wps_generate_prsn_demo.ipynb +++ b/notebooks/wps_generate_prsn_demo.ipynb @@ -11,11 +11,12 @@ }, { "cell_type": "code", - "execution_count": 2, + "execution_count": 1, "metadata": {}, "outputs": [], "source": [ "from birdy import WPSClient\n", + "import os\n", "from wps_tools.testing import get_target_url\n", "from netCDF4 import Dataset\n", "from tempfile import NamedTemporaryFile\n", @@ -24,14 +25,14 @@ }, { "cell_type": "code", - "execution_count": 3, + "execution_count": 2, "metadata": {}, "outputs": [ { "name": "stdout", "output_type": "stream", "text": [ - "Using thunderbird on https://docker-dev03.pcic.uvic.ca/twitcher/ows/proxy/thunderbird/wps\n" + "Using thunderbird on https://marble-dev01.pcic.uvic.ca/twitcher/ows/proxy/thunderbird/wps\n" ] } ], @@ -43,7 +44,7 @@ }, { "cell_type": "code", - "execution_count": 4, + "execution_count": 3, "metadata": {}, "outputs": [], "source": [ @@ -59,7 +60,7 @@ }, { "cell_type": "code", - "execution_count": 5, + "execution_count": 4, "metadata": {}, "outputs": [ { @@ -101,8 +102,8 @@ " Output Netcdf File\n", "dry_output : ComplexData:mimetype:`text/plain`\n", " File information\n", - "\u001b[0;31mFile:\u001b[0m ~/code/birds/thunderbird/notebooks/\n", - "\u001b[0;31mType:\u001b[0m method\n" + "\u001b[0;31mFile:\u001b[0m ~/code/thunderbird/notebooks/\n", + "\u001b[0;31mType:\u001b[0m method" ] }, "metadata": {}, @@ -123,14 +124,15 @@ }, { "cell_type": "code", - "execution_count": 6, + "execution_count": 5, "metadata": {}, "outputs": [], "source": [ "# Dry-run\n", - "pr_file_opendap = \"https://docker-dev03.pcic.uvic.ca/twitcher/ows/proxy/thredds/dodsC/datasets/storage/data/projects/comp_support/daccs/test-data/pr_day_BCCAQv2+ANUSPLIN300_NorESM1-M_historical+rcp26_r1i1p1_19500101-19500107.nc\"\n", - "tasmin_file_opendap = \"https://docker-dev03.pcic.uvic.ca/twitcher/ows/proxy/thredds/dodsC/datasets/storage/data/projects/comp_support/daccs/test-data/tasmin_day_BCCAQv2%2BANUSPLIN300_NorESM1-M_historical%2Brcp26_r1i1p1_19500101-19500107.nc\"\n", - "tasmax_file_opendap = \"https://docker-dev03.pcic.uvic.ca/twitcher/ows/proxy/thredds/dodsC/datasets/storage/data/projects/comp_support/daccs/test-data/tasmax_day_BCCAQv2%2BANUSPLIN300_NorESM1-M_historical%2Brcp26_r1i1p1_19500101-19500107.nc\"\n", + "thredds_host = os.getenv(\"THREDDS_HOST\", \"marble-dev01.pcic.uvic.ca\")\n", + "pr_file_opendap = f\"https://{thredds_host}/twitcher/ows/proxy/thredds/dodsC/datasets/storage/data/projects/comp_support/daccs/test-data/pr_day_BCCAQv2+ANUSPLIN300_NorESM1-M_historical+rcp26_r1i1p1_19500101-19500107.nc\"\n", + "tasmin_file_opendap = f\"https://{thredds_host}/twitcher/ows/proxy/thredds/dodsC/datasets/storage/data/projects/comp_support/daccs/test-data/tasmin_day_BCCAQv2%2BANUSPLIN300_NorESM1-M_historical%2Brcp26_r1i1p1_19500101-19500107.nc\"\n", + "tasmax_file_opendap = f\"https://{thredds_host}/twitcher/ows/proxy/thredds/dodsC/datasets/storage/data/projects/comp_support/daccs/test-data/tasmax_day_BCCAQv2%2BANUSPLIN300_NorESM1-M_historical%2Brcp26_r1i1p1_19500101-19500107.nc\"\n", "\n", "dry_output = thunderbird.generate_prsn(pr_file_opendap, tasmin_file_opendap, tasmax_file_opendap, chunk_size=50, dry_run=True)\n", "dry_output_data = dry_output.get(asobj=True)[0]" @@ -138,7 +140,7 @@ }, { "cell_type": "code", - "execution_count": 7, + "execution_count": 6, "metadata": {}, "outputs": [], "source": [ @@ -148,7 +150,7 @@ }, { "cell_type": "code", - "execution_count": 8, + "execution_count": 7, "metadata": {}, "outputs": [], "source": [ @@ -160,7 +162,7 @@ }, { "cell_type": "code", - "execution_count": 9, + "execution_count": 8, "metadata": {}, "outputs": [], "source": [ @@ -170,7 +172,7 @@ ], "metadata": { "kernelspec": { - "display_name": "Python 3", + "display_name": "Python 3 (ipykernel)", "language": "python", "name": "python3" }, @@ -184,7 +186,7 @@ "name": "python", "nbconvert_exporter": "python", "pygments_lexer": "ipython3", - "version": "3.8.5" + "version": "3.10.12" } }, "nbformat": 4, diff --git a/notebooks/wps_split_merged_climos_demo.ipynb b/notebooks/wps_split_merged_climos_demo.ipynb index ca6924e..1e60190 100644 --- a/notebooks/wps_split_merged_climos_demo.ipynb +++ b/notebooks/wps_split_merged_climos_demo.ipynb @@ -16,7 +16,7 @@ "outputs": [], "source": [ "from birdy import WPSClient\n", - "from pkg_resources import resource_filename\n", + "from importlib import resources\n", "import os\n", "from wps_tools.testing import get_target_url\n", "from wps_tools.output_handling import get_metalink_content\n", @@ -35,7 +35,7 @@ "name": "stdout", "output_type": "stream", "text": [ - "Using thunderbird on https://docker-dev03.pcic.uvic.ca/twitcher/ows/proxy/thunderbird/wps\n" + "Using thunderbird on https://marble-dev01.pcic.uvic.ca/twitcher/ows/proxy/thunderbird/wps\n" ] } ], @@ -84,8 +84,8 @@ "-------\n", "output : ComplexData:mimetype:`application/metalink+xml; version=4.0`\n", " Metalink object between output files\n", - "\u001b[0;31mFile:\u001b[0m ~/code/birds/thunderbird/\n", - "\u001b[0;31mType:\u001b[0m method\n" + "\u001b[0;31mFile:\u001b[0m ~/code/thunderbird/\n", + "\u001b[0;31mType:\u001b[0m method" ] }, "metadata": {}, @@ -111,11 +111,12 @@ "outputs": [], "source": [ "# Test local and opendap files\n", - "tasmax_climos_local = resource_filename('tests', 'data/tiny_downscaled_tasmax_climos.nc')\n", - "hydromodel_climos_opendap = \"https://docker-dev03.pcic.uvic.ca/twitcher/ows/proxy/thredds/dodsC/datasets/storage/data/projects/comp_support/daccs/test-data/tiny_hydromodel_gcm_climos.nc\"\n", - "multiple_inputs = [tasmax_climos_local, hydromodel_climos_opendap]\n", - "\n", - "output = thunderbird.split_merged_climos(multiple_inputs)" + "thredds_host = os.getenv(\"THREDDS_HOST\", \"marble-dev01.pcic.uvic.ca\")\n", + "ref = resources.files('tests') / 'data/tiny_downscaled_tasmax_climos.nc'\n", + "with resources.as_file(ref) as tasmax_climos_local:\n", + " hydromodel_climos_opendap = f\"https://{thredds_host}/twitcher/ows/proxy/thredds/dodsC/datasets/storage/data/projects/comp_support/daccs/test-data/tiny_hydromodel_gcm_climos.nc\"\n", + " multiple_inputs = [tasmax_climos_local, hydromodel_climos_opendap]\n", + " output = thunderbird.split_merged_climos(multiple_inputs)" ] }, { @@ -156,7 +157,7 @@ ], "metadata": { "kernelspec": { - "display_name": "Python 3", + "display_name": "Python 3 (ipykernel)", "language": "python", "name": "python3" }, @@ -170,7 +171,7 @@ "name": "python", "nbconvert_exporter": "python", "pygments_lexer": "ipython3", - "version": "3.8.5" + "version": "3.10.12" } }, "nbformat": 4, diff --git a/notebooks/wps_update_metadata_demo.ipynb b/notebooks/wps_update_metadata_demo.ipynb index cf6a1db..e2be448 100644 --- a/notebooks/wps_update_metadata_demo.ipynb +++ b/notebooks/wps_update_metadata_demo.ipynb @@ -15,11 +15,8 @@ "metadata": {}, "outputs": [], "source": [ - "import warnings\n", - "warnings.filterwarnings(\"ignore\", category=DeprecationWarning) \n", - "\n", "from birdy import WPSClient\n", - "from pkg_resources import resource_filename\n", + "from importlib import resources\n", "import os\n", "from wps_tools.testing import get_target_url\n", "from netCDF4 import Dataset\n", @@ -38,7 +35,7 @@ "name": "stdout", "output_type": "stream", "text": [ - "Using thunderbird on https://docker-dev03.pcic.uvic.ca/twitcher/ows/proxy/thunderbird/wps\n" + "Using thunderbird on https://marble-dev01.pcic.uvic.ca/twitcher/ows/proxy/thunderbird/wps\n" ] } ], @@ -97,8 +94,8 @@ "-------\n", "output : ComplexData:mimetype:`application/x-netcdf`\n", " Output Netcdf File\n", - "\u001b[0;31mFile:\u001b[0m ~/code/birds/thunderbird/\n", - "\u001b[0;31mType:\u001b[0m method\n" + "\u001b[0;31mFile:\u001b[0m ~/code/thunderbird/\n", + "\u001b[0;31mType:\u001b[0m method" ] }, "metadata": {}, @@ -131,7 +128,9 @@ " - address: University House 1 \n", " - Institution: <- institution\n", "'''\n", - "opendap_netcdf = \"https://docker-dev03.pcic.uvic.ca/twitcher/ows/proxy/thredds/dodsC/datasets/storage/data/projects/comp_support/daccs/test-data/gdd_annual_CanESM2_rcp85_r1i1p1_1951-2100.nc\"\n", + "\n", + "thredds_host = os.getenv(\"THREDDS_HOST\", \"marble-dev01.pcic.uvic.ca\")\n", + "opendap_netcdf = f\"https://{thredds_host}/twitcher/ows/proxy/thredds/dodsC/datasets/storage/data/projects/comp_support/daccs/test-data/tiny_hydromodel_gcm_climos.nc\"\n", "opendap_output = thunderbird.update_metadata(updates_string = updates_string, netcdf = opendap_netcdf)\n", "opendap_output_data = opendap_output.get(asobj=True)[0]" ] @@ -141,12 +140,22 @@ "execution_count": 6, "metadata": {}, "outputs": [], + "source": [ + "opendap_output_data = opendap_output.get(asobj=True)[0]" + ] + }, + { + "cell_type": "code", + "execution_count": 7, + "metadata": {}, + "outputs": [], "source": [ "# run update_metadata with yaml file and local netcdf inputs\n", - "updates_file = resource_filename('tests', 'metadata-conversion/simple-conversion.yaml')\n", - "local_netcdf = resource_filename('tests', 'data/gdd_annual_CanESM2_rcp85_r1i1p1_1951-2100.nc')\n", - "local_output = thunderbird.update_metadata(updates_file = updates_file, netcdf = local_netcdf)\n", - "local_output_data = local_output.get(asobj=True)[0]" + "ref_updates = resources.files('tests') / 'metadata-conversion/simple-conversion.yaml'\n", + "ref_netcdf = resources.files('tests') / 'data/tiny_hydromodel_gcm_climos.nc'\n", + "with resources.as_file(ref_updates) as updates_file, resources.as_file(ref_netcdf) as local_netcdf:\n", + " local_output = thunderbird.update_metadata(updates_file = updates_file, netcdf = local_netcdf)\n", + " local_output_data = local_output.get(asobj=True)[0]" ] }, { @@ -158,11 +167,11 @@ }, { "cell_type": "code", - "execution_count": 7, + "execution_count": 8, "metadata": {}, "outputs": [], "source": [ - "input_data = Dataset(\"https://docker-dev03.pcic.uvic.ca/twitcher/ows/proxy/thredds/dodsC/datasets/storage/data/projects/comp_support/daccs/test-data/gdd_annual_CanESM2_rcp85_r1i1p1_1951-2100.nc\")\n", + "input_data = Dataset(f\"https://{thredds_host}/twitcher/ows/proxy/thredds/dodsC/datasets/storage/data/projects/comp_support/daccs/test-data/gdd_annual_CanESM2_rcp85_r1i1p1_1951-2100.nc\")\n", "\n", "# Expected output metadata determined from the input yaml file\n", "# global:\n", @@ -179,7 +188,7 @@ }, { "cell_type": "code", - "execution_count": 8, + "execution_count": 9, "metadata": {}, "outputs": [], "source": [ @@ -196,7 +205,7 @@ }, { "cell_type": "code", - "execution_count": 9, + "execution_count": 10, "metadata": {}, "outputs": [], "source": [ @@ -207,7 +216,7 @@ ], "metadata": { "kernelspec": { - "display_name": "Python 3", + "display_name": "Python 3 (ipykernel)", "language": "python", "name": "python3" }, @@ -221,7 +230,7 @@ "name": "python", "nbconvert_exporter": "python", "pygments_lexer": "ipython3", - "version": "3.8.5" + "version": "3.10.12" } }, "nbformat": 4, From 5ab67f3e26eac48bbf14a8719f7bf79943d45f8e Mon Sep 17 00:00:00 2001 From: Eric Yvorchuk Date: Mon, 27 May 2024 13:45:22 -0700 Subject: [PATCH 14/32] Update docs --- docs/configuration.md | 6 +++--- docs/dev_guide.md | 16 ++++++++-------- docs/installation.md | 32 ++++++++++++++++---------------- 3 files changed, 27 insertions(+), 27 deletions(-) diff --git a/docs/configuration.md b/docs/configuration.md index 823ff8e..7276950 100644 --- a/docs/configuration.md +++ b/docs/configuration.md @@ -6,13 +6,13 @@ You can overwrite the default [PyWPS](http://pywps.org/) configuration by using command-line options. See the thunderbird help which options are available: ``` -(venv)$ thunderbird start --help +(thunderbird-py)$ thunderbird start --help --hostname HOSTNAME hostname in PyWPS configuration. --port PORT port in PyWPS configuration. ``` Start service with different hostname and port: ``` -(venv)$ thunderbird start --hostname localhost --port 5000 +(thunderbird-py)$ thunderbird start --hostname localhost --port 5000 ``` ## Use a custom configuration file @@ -33,5 +33,5 @@ level = DEBUG Start the service with your custom configuration: ``` # start the service with this configuration -(venv)$ thunderbird start -c etc/custom.cfg +(thunderbird-py)$ thunderbird start -c etc/custom.cfg ``` diff --git a/docs/dev_guide.md b/docs/dev_guide.md index 390198e..7e3feff 100644 --- a/docs/dev_guide.md +++ b/docs/dev_guide.md @@ -14,22 +14,22 @@ $ make docs ## Running tests Run tests using [`pytest`](https://docs.pytest.org/en/latest/). -First activate the `thunderbird` Python environment and install `pytest`. +First install the `thunderbird` Python environment. ``` -$ python3 -m venv venv -$ source venv/bin/activate -(venv)$ pip install -r requirements_dev.txt # if not already installed +$ poetry install --with=dev +$ poetry shell # OR -(venv)$ make install +$ make install +$ poetry shell ``` Run quick tests (skip slow and online): ``` -(venv)$ pytest -m 'not slow and not online'" +(thunderbird-py)$ pytest -m 'not slow and not online'" ``` Run all tests: ``` -(venv)$ pytest +(thunderbird-py)$ pytest ``` You can also run tests on the notebooks using the `Makefile`. @@ -39,7 +39,7 @@ $ make test-notebooks Check `black` formatting: ``` -(venv)$ black . +(thunderbird-py)$ black . ``` ## Run tests the lazy way diff --git a/docs/installation.md b/docs/installation.md index 363ea66..e4a7a85 100644 --- a/docs/installation.md +++ b/docs/installation.md @@ -12,41 +12,41 @@ $ git clone https://github.com/pacificclimate/thunderbird.git $ cd thunderbird ``` -Create Python environment named `venv`: +Install requirements and thunderbird app: ``` -$ python3 -m venv venv -$ source venv/bin/activate +$ poetry install +# OR +$ make install ``` -Install requirements: +For development you can use this command: ``` -(venv)$ pip install -r requirements.txt +$ poetry install --with=dev +# OR +$ make develop ``` -Install thunderbird app: +After creating the environment, you can enter it with this command: ``` -(venv)$ pip install -e . -# OR -$ make install +$ poetry shell ``` -For development you can use this command: +The environment name will be `thunderbird-py`, and you can use an environment with a different +Python version with the following command (provided said version is installed on your machine): ``` -$ pip install -e .[dev] -# OR -$ make develop +$ poetry env use ``` ## Start `thunderbird` PyWPS service After successful installation you can start the service using the `thunderbird` command-line. ``` -(venv)$ thunderbird --help # show help -(venv)$ thunderbird start # start service with default configuration +(thunderbird-py)$ thunderbird --help # show help +(thunderbird-py)$ thunderbird start # start service with default configuration # OR -(venv)$ thunderbird start --daemon # start service as daemon +(thunderbird-py)$ thunderbird start --daemon # start service as daemon loading configuration forked process id: 42 ``` From 7cd01190d4d2e07c15ee82875bc6dc6a6db57dc4 Mon Sep 17 00:00:00 2001 From: Eric Yvorchuk Date: Mon, 27 May 2024 15:05:00 -0700 Subject: [PATCH 15/32] Update dependencies marked by dependabot --- poetry.lock | 90 ++++++++------------ pyproject.toml | 7 +- thunderbird/processes/wps_update_metadata.py | 6 +- 3 files changed, 40 insertions(+), 63 deletions(-) diff --git a/poetry.lock b/poetry.lock index 8531239..9aac456 100644 --- a/poetry.lock +++ b/poetry.lock @@ -138,17 +138,6 @@ six = ">=1.12.0" astroid = ["astroid (>=1,<2)", "astroid (>=2,<4)"] test = ["astroid (>=1,<2)", "astroid (>=2,<4)", "pytest"] -[[package]] -name = "atpublic" -version = "4.1.0" -description = "Keep all y'all's __all__'s in sync" -optional = false -python-versions = ">=3.8" -files = [ - {file = "atpublic-4.1.0-py3-none-any.whl", hash = "sha256:df90de1162b1a941ee486f484691dc7c33123ee638ea5d6ca604061306e0fdde"}, - {file = "atpublic-4.1.0.tar.gz", hash = "sha256:d1c8cd931af7461f6d18bc6063383e8654d9e9ef19d58ee6dc01e8515bbf55df"}, -] - [[package]] name = "attrs" version = "22.2.0" @@ -1132,20 +1121,6 @@ mccabe = ">=0.7.0,<0.8.0" pycodestyle = ">=2.11.0,<2.12.0" pyflakes = ">=3.2.0,<3.3.0" -[[package]] -name = "flufl-enum" -version = "6.1.0" -description = "A Python enumeration package" -optional = false -python-versions = ">=3.8" -files = [ - {file = "flufl_enum-6.1.0-py3-none-any.whl", hash = "sha256:e9cf10e0f3f3985ddba6d831dd48ca376139d243f8c805b58600ab74675c4312"}, - {file = "flufl_enum-6.1.0.tar.gz", hash = "sha256:1def2f98963d1c75732f46ea5b14e81cff7f3f6b55bc5ac951d2f955fdf6fc7f"}, -] - -[package.dependencies] -atpublic = "*" - [[package]] name = "fqdn" version = "1.5.1" @@ -1292,6 +1267,20 @@ setproctitle = ["setproctitle"] testing = ["coverage", "eventlet", "gevent", "pytest", "pytest-cov"] tornado = ["tornado (>=0.2)"] +[[package]] +name = "humanize" +version = "4.9.0" +description = "Python humanize utilities" +optional = false +python-versions = ">=3.8" +files = [ + {file = "humanize-4.9.0-py3-none-any.whl", hash = "sha256:ce284a76d5b1377fd8836733b983bfb0b76f1aa1c090de2566fcf008d7f6ab16"}, + {file = "humanize-4.9.0.tar.gz", hash = "sha256:582a265c931c683a7e9b8ed9559089dea7edcf6cc95be39a3cbc2c5d5ac2bcfa"}, +] + +[package.extras] +tests = ["freezegun", "pytest", "pytest-cov"] + [[package]] name = "idna" version = "3.7" @@ -1748,23 +1737,23 @@ test = ["jupyter-server (>=2.0.0)", "pytest (>=7.0)", "pytest-jupyter[server] (> [[package]] name = "jupyterlab" -version = "2.1.5" +version = "2.2.10" description = "The JupyterLab notebook server extension." optional = false python-versions = ">=3.5" files = [ - {file = "jupyterlab-2.1.5-py3-none-any.whl", hash = "sha256:1ca00a008951ccfb197a3fd7a90bae8b1567dfeeab65d8552b19be9f8e9d7b01"}, - {file = "jupyterlab-2.1.5.tar.gz", hash = "sha256:ca7b92491c32b66ad97be4a44d79aa702e4b6c59167e4189d5ce8cc742b15298"}, + {file = "jupyterlab-2.2.10-py3-none-any.whl", hash = "sha256:b51fbd28b93f22d310207b8720ba3ee7e56da8bdf281fa2b92843680932f7262"}, + {file = "jupyterlab-2.2.10.tar.gz", hash = "sha256:802a57815a6af0f42dfd19a1b6b5d526f0605f1422c2d395cf837141975321e2"}, ] [package.dependencies] jinja2 = ">=2.10" -jupyterlab-server = ">=1.1.0,<2.0" +jupyterlab-server = ">=1.1.5,<2.0" notebook = ">=4.3.1" tornado = "<6.0.0 || >6.0.0,<6.0.1 || >6.0.1,<6.0.2 || >6.0.2" [package.extras] -docs = ["recommonmark", "sphinx", "sphinx-copybutton", "sphinx-rtd-theme"] +docs = ["jsx-lexer", "recommonmark", "sphinx", "sphinx-copybutton", "sphinx-rtd-theme"] test = ["pytest", "pytest-check-links", "requests", "virtualenv", "wheel"] [[package]] @@ -2727,17 +2716,6 @@ files = [ qa = ["flake8 (==5.0.4)", "mypy (==0.971)", "types-setuptools (==67.2.0.1)"] testing = ["docopt", "pytest"] -[[package]] -name = "pathlib" -version = "1.0.1" -description = "Object-oriented filesystem paths" -optional = false -python-versions = "*" -files = [ - {file = "pathlib-1.0.1-py3-none-any.whl", hash = "sha256:f35f95ab8b0f59e6d354090350b44a80a80635d22efdedfa84c7ad1cf0a74147"}, - {file = "pathlib-1.0.1.tar.gz", hash = "sha256:6940718dfc3eff4258203ad5021090933e5c04707d5ca8cc9e73c94a7894ea9f"}, -] - [[package]] name = "pathspec" version = "0.12.1" @@ -2928,13 +2906,13 @@ twisted = ["twisted"] [[package]] name = "prompt-toolkit" -version = "3.0.43" +version = "3.0.44" description = "Library for building powerful interactive command lines in Python" optional = false python-versions = ">=3.7.0" files = [ - {file = "prompt_toolkit-3.0.43-py3-none-any.whl", hash = "sha256:a11a29cb3bf0a28a387fe5122cdb649816a957cd9261dcedf8c9f1fef33eacf6"}, - {file = "prompt_toolkit-3.0.43.tar.gz", hash = "sha256:3527b7af26106cbc65a040bcc84839a3566ec1b051bb0bfe953631e704b0ff7d"}, + {file = "prompt_toolkit-3.0.44-py3-none-any.whl", hash = "sha256:205a20669633d042d3722a528b8e7cd3f4dbd9e1450935f596c2cc61166762dd"}, + {file = "prompt_toolkit-3.0.44.tar.gz", hash = "sha256:c1dfd082c4259964bc8bcce1f8460d9dbeb5d4a37bfc25b8082bc02cd41c8af6"}, ] [package.dependencies] @@ -3270,21 +3248,21 @@ files = [ [[package]] name = "pywps" -version = "4.2.9" +version = "4.5.0" description = "PyWPS is an implementation of the Web Processing Service standard from the Open Geospatial Consortium. PyWPS is written in Python." optional = false -python-versions = "*" +python-versions = ">=3.6, <4" files = [ - {file = "pywps-4.2.9.tar.gz", hash = "sha256:a9a0c1b586e3711f30ac8dfb3b78452f1e10873e9615ffe40033c34dba89bdad"}, + {file = "pywps-4.5.0.tar.gz", hash = "sha256:2d9e2711c68a01a7f9b095faa110bc3471f0932b5e211bde981757e1253c1d90"}, ] [package.dependencies] -"flufl.enum" = "*" +humanize = "*" jinja2 = "*" jsonschema = "*" lxml = "*" +MarkupSafe = "*" owslib = "*" -pathlib = "*" python-dateutil = "*" requests = "*" SQLAlchemy = "*" @@ -4431,17 +4409,19 @@ test = ["websockets"] [[package]] name = "werkzeug" -version = "1.0.1" +version = "2.2.3" description = "The comprehensive WSGI web application library." optional = false -python-versions = ">=2.7, !=3.0.*, !=3.1.*, !=3.2.*, !=3.3.*, !=3.4.*" +python-versions = ">=3.7" files = [ - {file = "Werkzeug-1.0.1-py2.py3-none-any.whl", hash = "sha256:2de2a5db0baeae7b2d2664949077c2ac63fbd16d98da0ff71837f7d1dea3fd43"}, - {file = "Werkzeug-1.0.1.tar.gz", hash = "sha256:6c80b1e5ad3665290ea39320b91e1be1e0d5f60652b964a3070216de83d2e47c"}, + {file = "Werkzeug-2.2.3-py3-none-any.whl", hash = "sha256:56433961bc1f12533306c624f3be5e744389ac61d722175d543e1751285da612"}, + {file = "Werkzeug-2.2.3.tar.gz", hash = "sha256:2e1ccc9417d4da358b9de6f174e3ac094391ea1d4fbef2d667865d819dfd0afe"}, ] +[package.dependencies] +MarkupSafe = ">=2.1.1" + [package.extras] -dev = ["coverage", "pallets-sphinx-themes", "pytest", "pytest-timeout", "sphinx", "sphinx-issues", "tox"] watchdog = ["watchdog"] [[package]] @@ -4678,4 +4658,4 @@ testing = ["big-O", "jaraco.functools", "jaraco.itertools", "jaraco.test", "more [metadata] lock-version = "2.0" python-versions = ">=3.9,<4" -content-hash = "9e08cdc6c2f732707d3fafb619e946c7625be788736257f10e390f00b4b232db" +content-hash = "0b6dce2686c7e97f98bd0305092af14be34f8fc0fd3b9ad5fe663b186108700d" diff --git a/pyproject.toml b/pyproject.toml index eb3a442..877bdda 100644 --- a/pyproject.toml +++ b/pyproject.toml @@ -14,6 +14,7 @@ license = "GPL3" readme = "README.md" homepage = "http://www.pacificclimate.org/" repository = "https://github.com/pacificclimate/thunderbird" +keywords = ["wps", "pywps", "birdhouse", "thunderbird"] classifiers = [ "Development Status :: 3 - Alpha", "Intended Audience :: Developers", @@ -52,10 +53,10 @@ jinja2 = ">=2.11.3,<3.1.0" netcdf4 = "1.6.2" numpy = "^1.20.0" psutil = "5.9.8" -pywps = "4.2.9" +pywps = "4.5.0" xarray = "^2024.2.0" nchelpers = { version = "^5.5.11", source = "pcic" } -werkzeug = "1.0.1" +werkzeug = "2.2.3" wps-tools = { version = "^2.1.1", source = "pcic" } cdo = "1.6.0" poetry-dotenv-plugin = "^0.2.0" @@ -75,7 +76,7 @@ twine = "^5.1.0" cruft = "^2.15.0" nbclient = ">=0.5.10,<0.6.0" black = "22.3.0" -jupyterlab = "2.1.5" +jupyterlab = "2.2.10" ipywidgets = "7.5.1" nodejs = "0.1.1" birdhouse-birdy = "0.8.4" diff --git a/thunderbird/processes/wps_update_metadata.py b/thunderbird/processes/wps_update_metadata.py index 422a378..95e830e 100644 --- a/thunderbird/processes/wps_update_metadata.py +++ b/thunderbird/processes/wps_update_metadata.py @@ -114,11 +114,7 @@ def updates_instruction_generator(self, request): holds the path to the origial file path. """ if "updates_file" in request.inputs.keys(): - if vars(request.inputs["updates_file"][0])["_file"] != None: - updates = request.inputs["updates_file"][ - 0 - ].file # For running in localhost - elif vars(request.inputs["updates_file"][0])["_data"] != None: + if request.inputs["updates_file"][0].data != None: updates = request.inputs["updates_file"][ 0 ].data # For running in localhost From b4cd1a84d52feb48e0a08669a0ab3f1adc1e1696 Mon Sep 17 00:00:00 2001 From: Eric Yvorchuk Date: Mon, 27 May 2024 15:21:57 -0700 Subject: [PATCH 16/32] Update version in .cruft.json --- .cruft.json | 4 ++-- 1 file changed, 2 insertions(+), 2 deletions(-) diff --git a/.cruft.json b/.cruft.json index 5a066f0..dfb1af6 100644 --- a/.cruft.json +++ b/.cruft.json @@ -11,7 +11,7 @@ "project_repo_name": "thunderbird", "project_readthedocs_name": "thunderbird", "project_short_description": "A Web Processing Service for Climate Explorer data preparation", - "version": "0.6.0", + "version": "1.2.3", "open_source_license": "GNU General Public License v3", "http_port": "5000", "_copy_without_render": [ @@ -20,4 +20,4 @@ "_template": "https://github.com/bird-house/cookiecutter-birdhouse" } } -} \ No newline at end of file +} From 62484da4217bd62de54112286720f43287806052 Mon Sep 17 00:00:00 2001 From: Eric Yvorchuk Date: Mon, 27 May 2024 15:45:16 -0700 Subject: [PATCH 17/32] Add more pytest options --- pyproject.toml | 2 ++ 1 file changed, 2 insertions(+) diff --git a/pyproject.toml b/pyproject.toml index 877bdda..fdcfd20 100644 --- a/pyproject.toml +++ b/pyproject.toml @@ -93,6 +93,8 @@ requires = ["poetry-core"] build-backend = "poetry.core.masonry.api" [tool.pytest.ini_options] +addopts = "--strict --tb=native" +python_files = ["test_*.py"] markers = [ "online: marks tests that use online resources (deselect with '-m \"not online\"')", "slow: marks tests that are slow (deselect with '-m \"not slow\"')", From 7bed4aab777af55f96e99a5eed3a2c21fe838b16 Mon Sep 17 00:00:00 2001 From: Eric Yvorchuk Date: Mon, 27 May 2024 15:47:23 -0700 Subject: [PATCH 18/32] Remove files for previous installation process --- requirements.txt | 12 --------- requirements_dev.txt | 22 ----------------- setup.cfg | 34 -------------------------- setup.py | 58 -------------------------------------------- 4 files changed, 126 deletions(-) delete mode 100644 requirements.txt delete mode 100644 requirements_dev.txt delete mode 100644 setup.cfg delete mode 100644 setup.py diff --git a/requirements.txt b/requirements.txt deleted file mode 100644 index 3efc73e..0000000 --- a/requirements.txt +++ /dev/null @@ -1,12 +0,0 @@ -ce-dataprep==0.8.8 -cftime==1.1.3 -click==7.1.2 -jinja2>=2.11.3,<3.1.0 -netCDF4==1.5.6 -psutil==5.7.0 -pywps==4.2.9 -xarray==0.15.1 -nchelpers==5.5.7 -werkzeug==1.0.1 -wps-tools==2.0.0 -cdo==1.5.4 diff --git a/requirements_dev.txt b/requirements_dev.txt deleted file mode 100644 index aede0e6..0000000 --- a/requirements_dev.txt +++ /dev/null @@ -1,22 +0,0 @@ -pytest>=6.0 -flake8 -pytest-flake8 -ipython -pytest-notebook -nbsphinx -nbval>=0.9.6 -nbconvert -Sphinx==2.4.4 -bumpversion -twine -# Changing dependencies above this comment will create merge conflicts when updating the cookiecutter template with cruft. Add extra requirements below this line. -cruft -nbclient~=0.5.10 -black==19.10b0 -jupyterlab==2.1.5 -ipywidgets==7.5.1 -nodejs==0.1.1 -birdhouse-birdy==0.6.9 -beautifulsoup4==4.9.3 -notebook>=6.1.5 # not directly required, pinned by Snyk to avoid a vulnerability -pygments>=2.7.4 # not directly required, pinned by Snyk to avoid a vulnerability diff --git a/setup.cfg b/setup.cfg deleted file mode 100644 index db6a9d2..0000000 --- a/setup.cfg +++ /dev/null @@ -1,34 +0,0 @@ -[bumpversion] -current_version = 0.6.0 -commit = True -tag = True - -[metadata] -description-file = README.md - -[options] -include-package-data = True - -[options.package_data] -thunderbird = tests/data/*.nc, tests/metadata-conversion/*.yaml - -[bumpversion:file:thunderbird/__version__.py] -search = __version__ = '{current_version}' -replace = __version__ = '{new_version}' - -[bumpversion:file:Dockerfile] -search = Version="{current_version}" -replace = Version="{new_version}" - -[bumpversion:file:.cruft.json] -search = "version": "{current_version}", -replace = "version": "{new_version}", - -[tool:pytest] -addopts = - --strict - --tb=native -python_files = test_*.py -markers = - online: mark test to need internet connection - slow: mark test to be slow diff --git a/setup.py b/setup.py deleted file mode 100644 index a1ee5d2..0000000 --- a/setup.py +++ /dev/null @@ -1,58 +0,0 @@ -#!/usr/bin/env python -# -*- coding: utf-8 -*- - -"""The setup script.""" - -import os - -from setuptools import setup, find_packages - -here = os.path.abspath(os.path.dirname(__file__)) -README = open(os.path.join(here, "README.md")).read() -CHANGES = open(os.path.join(here, "CHANGES.md")).read() -REQUIRES_PYTHON = ">=3.7.0" - -about = {} -with open(os.path.join(here, "thunderbird", "__version__.py"), "r") as f: - exec(f.read(), about) - -reqs = [line.strip() for line in open("requirements.txt")] -dev_reqs = [line.strip() for line in open("requirements_dev.txt")] - -classifiers = [ - "Development Status :: 3 - Alpha", - "Intended Audience :: Developers", - "Intended Audience :: Science/Research", - "Operating System :: MacOS :: MacOS X", - "Operating System :: POSIX", - "Programming Language :: Python", - "Natural Language :: English", - "Programming Language :: Python :: 3", - "Programming Language :: Python :: 3.7", - "Programming Language :: Python :: 3.8", - "Topic :: Scientific/Engineering :: Atmospheric Science", - "License :: OSI Approved :: GNU General Public License v3 (GPLv3)", -] - -setup( - name="thunderbird-daccs", - version=about["__version__"], - description="A Web Processing Service for Climate Explorer data preparation", - long_description=README + "\n\n" + CHANGES, - author=about["__author__"], - author_email=about["__email__"], - url="https://github.com/pacificclimate/thunderbird", - python_requires=REQUIRES_PYTHON, - classifiers=classifiers, - license="GNU General Public License v3", - keywords="wps pywps birdhouse thunderbird", - packages=find_packages(), - package_data={ - "thunderbird": ["tests/data/*.nc", "tests/metadata-conversion/*.yaml"], - "tests": ["data/*.nc", "metadata-conversion/*.yaml"], - }, - include_package_data=True, - install_requires=reqs, - extras_require={"dev": dev_reqs}, # pip install ".[dev]" - entry_points={"console_scripts": ["thunderbird=thunderbird.cli:cli"]}, -) From 015f983b3541dd1a8713dd21cffcf342f5cab759 Mon Sep 17 00:00:00 2001 From: Eric Yvorchuk Date: Mon, 27 May 2024 15:47:48 -0700 Subject: [PATCH 19/32] Use dedicated bumpversion config file --- .bumpversion.cfg | 16 ++++++++++++++++ docs/dev_guide.md | 6 +++--- 2 files changed, 19 insertions(+), 3 deletions(-) create mode 100644 .bumpversion.cfg diff --git a/.bumpversion.cfg b/.bumpversion.cfg new file mode 100644 index 0000000..1afd2a8 --- /dev/null +++ b/.bumpversion.cfg @@ -0,0 +1,16 @@ +[bumpversion] +current_version = 1.2.3 +commit = True +tag = True + +[bumpversion:file:thunderbird/__version__.py] +search = __version__ = "{current_version}" +replace = __version__ = "{new_version}" + +[bumpversion:file:Dockerfile] +search = Version="{current_version}" +replace = Version="{new_version}" + +[bumpversion:file:.cruft.json] +search = "version": "{current_version}" +replace = "version": "{new_version}" diff --git a/docs/dev_guide.md b/docs/dev_guide.md index 7e3feff..bb56c83 100644 --- a/docs/dev_guide.md +++ b/docs/dev_guide.md @@ -55,9 +55,9 @@ Make a new version of `thunderbird` in the following steps: * Make sure everything is committed to GitHub. * Update `CHANGES.md` with the next version. -* Dry Run: `bumpversion --dry-run --verbose --new-version 0.8.1 patch` -* Do it: `bumpversion --new-version 0.8.1 patch` -* ... or: `bumpversion --new-version 0.9.0 minor` +* Dry Run: `bumpversion --dry-run --verbose patch` +* Do it: `bumpversion patch` +* ... or: `bumpversion minor` * Push it: `git push` * Push tag: `git push --tags` From 3c4b6f38ad9995741538c19ff2cea8bf81bb1c4b Mon Sep 17 00:00:00 2001 From: Eric Yvorchuk Date: Mon, 27 May 2024 15:55:44 -0700 Subject: [PATCH 20/32] Add pyproject.toml to .bumpversion.cfg --- .bumpversion.cfg | 4 ++++ 1 file changed, 4 insertions(+) diff --git a/.bumpversion.cfg b/.bumpversion.cfg index 1afd2a8..6f36628 100644 --- a/.bumpversion.cfg +++ b/.bumpversion.cfg @@ -7,6 +7,10 @@ tag = True search = __version__ = "{current_version}" replace = __version__ = "{new_version}" +[bumpversion:file:pyproject.toml] +search = version = "{current_version}" +replace = version = "{new_version}" + [bumpversion:file:Dockerfile] search = Version="{current_version}" replace = Version="{new_version}" From a36deca86f33b2b67800ca8ceb2a21e85abdf773 Mon Sep 17 00:00:00 2001 From: Eric Yvorchuk Date: Tue, 28 May 2024 09:07:59 -0700 Subject: [PATCH 21/32] Clarify bumpversion section of dev docs --- docs/dev_guide.md | 5 ++--- 1 file changed, 2 insertions(+), 3 deletions(-) diff --git a/docs/dev_guide.md b/docs/dev_guide.md index bb56c83..bdcf7a6 100644 --- a/docs/dev_guide.md +++ b/docs/dev_guide.md @@ -54,11 +54,10 @@ $ make lint Make a new version of `thunderbird` in the following steps: * Make sure everything is committed to GitHub. -* Update `CHANGES.md` with the next version. +* Update `CHANGES.md` with the next version and commit. * Dry Run: `bumpversion --dry-run --verbose patch` * Do it: `bumpversion patch` * ... or: `bumpversion minor` -* Push it: `git push` -* Push tag: `git push --tags` +* Push it: `git push --tags` See the [bumpversion](https://pypi.org/project/bumpversion/) documentation for details. From 89a4b4dad52187417f3e1fbc474f73bb4c8350ad Mon Sep 17 00:00:00 2001 From: Eric Yvorchuk Date: Tue, 28 May 2024 09:15:19 -0700 Subject: [PATCH 22/32] Fix commands for testing using Makefile --- docs/dev_guide.md | 4 ++-- 1 file changed, 2 insertions(+), 2 deletions(-) diff --git a/docs/dev_guide.md b/docs/dev_guide.md index bdcf7a6..3011dc3 100644 --- a/docs/dev_guide.md +++ b/docs/dev_guide.md @@ -19,7 +19,7 @@ First install the `thunderbird` Python environment. $ poetry install --with=dev $ poetry shell # OR -$ make install +$ make develop $ poetry shell ``` @@ -34,7 +34,7 @@ Run all tests: You can also run tests on the notebooks using the `Makefile`. ``` -$ make test-notebooks +$ make test-notebooks-prod ``` Check `black` formatting: From 1a47c8c65ba73a18dd1d62f69d5fba4c4e5994ac Mon Sep 17 00:00:00 2001 From: Eric Yvorchuk Date: Tue, 28 May 2024 14:12:29 -0700 Subject: [PATCH 23/32] Update pywps to 4.5.2 --- poetry.lock | 327 ++++++++++++++++++++++++++++++++++++++++--------- pyproject.toml | 2 +- 2 files changed, 267 insertions(+), 62 deletions(-) diff --git a/poetry.lock b/poetry.lock index 9aac456..ede7eee 100644 --- a/poetry.lock +++ b/poetry.lock @@ -1,4 +1,4 @@ -# This file is automatically @generated by Poetry 1.7.1 and should not be changed by hand. +# This file is automatically @generated by Poetry 1.8.3 and should not be changed by hand. 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"click-plugins-1.1.1.tar.gz", hash = "sha256:46ab999744a9d831159c3411bb0c79346d94a444df9a3a3742e9ed63645f264b"}, + {file = "click_plugins-1.1.1-py2.py3-none-any.whl", hash = "sha256:5d262006d3222f5057fd81e1623d4443e41dcda5dc815c06b442aa3c02889fc8"}, +] + +[package.dependencies] +click = ">=4.0" + +[package.extras] +dev = ["coveralls", "pytest (>=3.6)", "pytest-cov", "wheel"] + +[[package]] +name = "cligj" +version = "0.7.2" +description = "Click params for commmand line interfaces to GeoJSON" +optional = false +python-versions = ">=2.7, !=3.0.*, !=3.1.*, !=3.2.*, <4" +files = [ + {file = "cligj-0.7.2-py3-none-any.whl", hash = "sha256:c1ca117dbce1fe20a5809dc96f01e1c2840f6dcc939b3ddbb1111bf330ba82df"}, + {file = "cligj-0.7.2.tar.gz", hash = "sha256:a4bc13d623356b373c2c27c53dbd9c68cae5d526270bfa71f6c6fa69669c6b27"}, +] + +[package.dependencies] +click = ">=4.0" + +[package.extras] +test = ["pytest-cov"] + [[package]] name = "colorama" version = "0.4.6" @@ -727,63 +771,63 @@ rich = "*" 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""" if "updates_file" in request.inputs.keys(): - if request.inputs["updates_file"][0].data != None: + if not os.path.exists("/.dockerenv"): updates = request.inputs["updates_file"][ 0 ].data # For running in localhost From d7d20320e5a77b0b32ade1bc8e2e258834a4dfc7 Mon Sep 17 00:00:00 2001 From: Eric Yvorchuk Date: Tue, 28 May 2024 16:08:46 -0700 Subject: [PATCH 25/32] Install system dependencies first in Dockerfile to cache layer --- Dockerfile | 6 +++--- 1 file changed, 3 insertions(+), 3 deletions(-) diff --git a/Dockerfile b/Dockerfile index 1818476..991e404 100644 --- a/Dockerfile +++ b/Dockerfile @@ -4,13 +4,13 @@ LABEL Maintainer=https://github.com/pacificclimate/thunderbird Description="thun ENV DEBIAN_FRONTEND=noninteractive ENV PIP_INDEX_URL="https://pypi.pacificclimate.org/simple/" -COPY . /tmp -WORKDIR /tmp - RUN apt-get update && \ apt-get install -y cdo curl libhdf5-serial-dev netcdf-bin libnetcdf-dev && \ rm -rf /var/lib/apt/lists/* +COPY . /tmp +WORKDIR /tmp + RUN curl -sSL https://install.python-poetry.org | python3 - ENV PATH=/root/.local/bin:$PATH RUN poetry install From bdcd5308454ba3447d61e0f40a28a311b4351989 Mon Sep 17 00:00:00 2001 From: Eric Yvorchuk Date: Wed, 29 May 2024 08:51:44 -0700 Subject: [PATCH 26/32] Ensure full test suite works in CI before merging --- .github/workflows/python-ci.yml | 2 +- 1 file changed, 1 insertion(+), 1 deletion(-) diff --git a/.github/workflows/python-ci.yml b/.github/workflows/python-ci.yml index 99243e6..02f3ac9 100644 --- a/.github/workflows/python-ci.yml +++ b/.github/workflows/python-ci.yml @@ -25,7 +25,7 @@ jobs: poetry env use python${{ matrix.python-version }} make install-ci - name: Test with pytest (full) - if: github.ref == 'refs/heads/master' + #if: github.ref == 'refs/heads/master' run: | make test-all - name: Test with pytest (fast) From 99e5d85775414a7fe06798b23afe85274ec9112e Mon Sep 17 00:00:00 2001 From: Eric Yvorchuk Date: Wed, 29 May 2024 09:20:59 -0700 Subject: [PATCH 27/32] Omit online tests for running full test suite in CI --- .github/workflows/python-ci.yml | 2 +- Makefile | 5 +++++ 2 files changed, 6 insertions(+), 1 deletion(-) diff --git a/.github/workflows/python-ci.yml b/.github/workflows/python-ci.yml index 02f3ac9..bc60326 100644 --- a/.github/workflows/python-ci.yml +++ b/.github/workflows/python-ci.yml @@ -27,7 +27,7 @@ jobs: - name: Test with pytest (full) #if: github.ref == 'refs/heads/master' run: | - make test-all + make test-not-online - name: Test with pytest (fast) if: github.ref != 'refs/heads/master' run: | diff --git a/Makefile b/Makefile index 170b9c6..0d70231 100644 --- a/Makefile +++ b/Makefile @@ -128,6 +128,11 @@ test-all: @echo "Running all tests (including slow and online tests) ..." @bash -c 'poetry run pytest -v tests/' +.PHONY: test-not-online +test-all: + @echo "Running tests (including slow but excluding online tests) ..." + @bash -c 'poetry run pytest -v -m "not online" tests/' + .PHONY: notebook-sanitizer notebook-sanitizer: @echo "Copying notebook output sanitizer ..." From 994391a1dd777fabeb1a3ac6768eccdd19c8e232 Mon Sep 17 00:00:00 2001 From: Eric Yvorchuk Date: Wed, 29 May 2024 09:23:42 -0700 Subject: [PATCH 28/32] Fix Makefile --- Makefile | 6 +++--- 1 file changed, 3 insertions(+), 3 deletions(-) diff --git a/Makefile b/Makefile index 0d70231..9c061fe 100644 --- a/Makefile +++ b/Makefile @@ -129,9 +129,9 @@ test-all: @bash -c 'poetry run pytest -v tests/' .PHONY: test-not-online -test-all: - @echo "Running tests (including slow but excluding online tests) ..." - @bash -c 'poetry run pytest -v -m "not online" tests/' +test-not-online: + @echo "Running tests (including slow but excluding online tests) ..." + @bash -c 'poetry run pytest -v -m "not online" tests/' .PHONY: notebook-sanitizer notebook-sanitizer: From 101da749a54510a7a2c50439cce497142158c60c Mon Sep 17 00:00:00 2001 From: Eric Yvorchuk Date: Wed, 29 May 2024 09:33:56 -0700 Subject: [PATCH 29/32] Uncomment check for master branch --- .github/workflows/python-ci.yml | 2 +- 1 file changed, 1 insertion(+), 1 deletion(-) diff --git a/.github/workflows/python-ci.yml b/.github/workflows/python-ci.yml index bc60326..78ef2b0 100644 --- a/.github/workflows/python-ci.yml +++ b/.github/workflows/python-ci.yml @@ -25,7 +25,7 @@ jobs: poetry env use python${{ matrix.python-version }} make install-ci - name: Test with pytest (full) - #if: github.ref == 'refs/heads/master' + if: github.ref == 'refs/heads/master' run: | make test-not-online - name: Test with pytest (fast) From 251b9b39533cf43ce794c9fe6f437fc0d62165ff Mon Sep 17 00:00:00 2001 From: Eric Yvorchuk Date: Wed, 29 May 2024 13:51:24 -0700 Subject: [PATCH 30/32] Replace THREDDS_HOST with DACCS_HOST --- .env | 2 +- docs/formatted_demos/wps_decompose_flow_vectors_demo.html | 4 ++-- docs/formatted_demos/wps_generate_climos_demo.html | 6 +++--- docs/formatted_demos/wps_generate_prsn_demo.html | 8 ++++---- docs/formatted_demos/wps_split_merged_climos_demo.html | 4 ++-- docs/formatted_demos/wps_update_metadata_demo.html | 6 +++--- notebooks/wps_decompose_flow_vectors_demo.ipynb | 4 ++-- notebooks/wps_generate_climos_demo.ipynb | 6 +++--- notebooks/wps_generate_prsn_demo.ipynb | 8 ++++---- notebooks/wps_split_merged_climos_demo.ipynb | 4 ++-- notebooks/wps_update_metadata_demo.ipynb | 6 +++--- thunderbird/utils.py | 2 +- 12 files changed, 30 insertions(+), 30 deletions(-) diff --git a/.env b/.env index 34fc6f3..bc50e8b 100644 --- a/.env +++ b/.env @@ -1 +1 @@ -THREDDS_HOST="marble-dev01.pcic.uvic.ca" +DACCS_HOST="marble-dev01.pcic.uvic.ca" diff --git a/docs/formatted_demos/wps_decompose_flow_vectors_demo.html b/docs/formatted_demos/wps_decompose_flow_vectors_demo.html index 704afea..d8ba989 100644 --- a/docs/formatted_demos/wps_decompose_flow_vectors_demo.html +++ b/docs/formatted_demos/wps_decompose_flow_vectors_demo.html @@ -7667,8 +7667,8 @@

In [5]: