move configuration into pyproject.toml (#134)

* move configuration into `pyproject.toml` * update test workflows * update reference files * update test * rename tests * test fix * `fail-fast: true` * test fix
noaa-ocs-modeling · Apr 21, 2022 · 379b111 · 379b111
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diff --git a/.github/workflows/build.yml b/.github/workflows/build.yml
@@ -6,62 +6,19 @@ on:
       - published
 
 jobs:
-  build_wheels:
-    name: build wheel
-    runs-on: ${{ matrix.os }}
-    strategy:
-      matrix:
-        os: [ ubuntu-latest ]
-        python-version: [ '3.x' ]
-    steps:
-      - name: checkout repository
-        uses: actions/checkout@v2
-      - name: install Python
-        uses: actions/setup-python@v2
-        with:
-          python-version: ${{ matrix.python-version }}
-      - name: load cached Python installation
-        id: cache
-        uses: actions/cache@v2
-        with:
-          path: ${{ env.pythonLocation }}
-          key: build-${{ runner.os }}-${{ env.pythonLocation }}-${{ hashFiles('pyproject.toml', 'setup.*') }}
-      - name: build wheel
-        run: pip wheel . -w dist --no-deps
-      - name: save wheel
-        uses: actions/upload-artifact@v2
-        with:
-          name: build
-          path: ./dist/*.whl
-  build_sdist:
-    name: package source
+  publish:
+    name: publish package to PyPI
     runs-on: ubuntu-latest
     steps:
       - name: checkout repository
         uses: actions/checkout@v2
-      - name: install Python
-        uses: actions/setup-python@v2
-      - name: install dependencies
+      - name: install Poetry
+        uses: abatilo/actions-poetry@v2.1.3
+      - name: install Dunamai
         run: pip install dunamai
-      - name: package source
-        run: python setup.py sdist
-      - name: save source package
-        uses: actions/upload-artifact@v2
-        with:
-          name: build
-          path: ./dist/*.tar.gz
-  upload_pypi:
-    name: publish to PyPI
-    needs: [ build_wheels, build_sdist ]
-    runs-on: ubuntu-latest
-    steps:
-      - name: retrieve wheel(s) and source
-        uses: actions/download-artifact@v2
-        with:
-          name: build
-          path: dist
-      - name: upload wheel(s) and source
-        uses: pypa/[email protected]
-        with:
-          user: __token__
-          password: ${{ secrets.PYPI_TOKEN }}
+      - name: extract version from VCS
+        run: poetry version $(dunamai from any)
+      - name: build wheel and source
+        run: poetry build
+      - name: upload wheel and source
+        run: poetry publish --username __token__ --password ${{ secrets.PYPI_TOKEN }}
diff --git a/.github/workflows/quick_test.yml b/.github/workflows/quick_test.yml
@@ -0,0 +1,55 @@
+name: quick test
+
+on:
+  push:
+    branches-ignore:
+      - main
+    paths:
+      - '**.py'
+      - '.github/workflows/quick_test.yml'
+      - 'pyproject.toml'
+
+jobs:
+  lint:
+    name: lint
+    runs-on: ubuntu-latest
+    steps:
+      - name: clone repository
+        uses: actions/checkout@v2
+      - name: install Python
+        uses: actions/setup-python@v2
+      - name: load cached Python installation
+        id: cache
+        uses: actions/cache@v2
+        with:
+          path: ${{ env.pythonLocation }}
+          key: lint-${{ runner.os }}-${{ env.pythonLocation }}-${{ hashFiles('pyproject.toml') }}
+      - name: install linters
+        run: pip install flake8 oitnb
+      - name: lint with flake8
+        run: |
+          # stop the build if there are Python syntax errors or undefined names
+          flake8 . --count --select=E9,F63,F7,F82 --show-source --statistics
+          # exit-zero treats all errors as warnings. The GitHub editor is 127 chars wide
+          flake8 . --count --exit-zero --max-complexity=10 --max-line-length=127 --statistics
+      - name: lint with oitnb
+        run: oitnb . --check
+  test:
+    needs: lint
+    name: quick test
+    runs-on: ubuntu-latest
+    steps:
+      - name: clone repository
+        uses: actions/checkout@v2
+      - name: install Python
+        uses: actions/setup-python@v2
+      - name: load cached Python installation
+        id: cache
+        uses: actions/cache@v2
+        with:
+          path: ${{ env.pythonLocation }}
+          key: test-${{ runner.os }}-${{ env.pythonLocation }}-${{ hashFiles('pyproject.toml') }}
+      - name: install dependencies
+        run: pip install ".[testing]"
+      - name: run tests
+        run: pytest --numprocesses auto
diff --git a/.github/workflows/tests.yml b/.github/workflows/tests.yml
@@ -1,44 +1,50 @@
 name: tests
 
-on: [ push ]
+on:
+  push:
+    branches:
+      - main
+    paths:
+      - '**.py'
+      - '.github/workflows/tests.yml'
+      - 'pyproject.toml'
+  pull_request:
+    branches:
+      - main
 
 jobs:
   lint:
     name: lint
     runs-on: ubuntu-latest
-    strategy:
-      matrix:
-        python-version: [ '3.x' ]
     steps:
       - name: clone repository
         uses: actions/checkout@v2
       - name: install Python
         uses: actions/setup-python@v2
-        with:
-          python-version: ${{ matrix.python-version }}
       - name: load cached Python installation
         id: cache
         uses: actions/cache@v2
         with:
           path: ${{ env.pythonLocation }}
-          key: lint-${{ runner.os }}-${{ env.pythonLocation }}-${{ hashFiles('pyproject.toml', 'setup.*') }}
-      - name: install dependencies
-        if: steps.cache.outputs.cache-hit != 'true'
-        run: pip install ".[development]"
+          key: lint-${{ runner.os }}-${{ env.pythonLocation }}-${{ hashFiles('pyproject.toml') }}
+      - name: install linters
+        run: pip install flake8 oitnb
       - name: lint with flake8
         run: |
           # stop the build if there are Python syntax errors or undefined names
           flake8 . --count --select=E9,F63,F7,F82 --show-source --statistics
           # exit-zero treats all errors as warnings. The GitHub editor is 127 chars wide
           flake8 . --count --exit-zero --max-complexity=10 --max-line-length=127 --statistics
+      - name: lint with oitnb
+        run: oitnb . --check
   test:
     needs: lint
     name: test
     runs-on: ${{ matrix.os }}
     strategy:
       matrix:
-        os: [ ubuntu-latest ]
-        python-version: [ '3.7', '3.x' ]
+        os: [ ubuntu-latest, macos-latest ]
+        python-version: [ '3.7', '3.8', '3.9', '3.x' ]
     steps:
       - name: clone repository
         uses: actions/checkout@v2
@@ -51,18 +57,33 @@ jobs:
         uses: actions/cache@v2
         with:
           path: ${{ env.pythonLocation }}
-          key: test-${{ runner.os }}-${{ env.pythonLocation }}-${{ hashFiles('pyproject.toml', 'setup.*') }}
+          key: test-${{ runner.os }}-${{ env.pythonLocation }}-${{ hashFiles('pyproject.toml') }}
       - name: install dependencies
-        if: steps.cache.outputs.cache-hit != 'true'
         run: pip install ".[testing]"
       - name: run tests
-        if: matrix.python-version != '3.x' || matrix.os != 'ubuntu-latest'
         run: pytest --numprocesses auto
+  test_with_coverage:
+    needs: [ lint, test ]
+    name: test with coverage
+    runs-on: ubuntu-latest
+    steps:
+      - name: clone repository
+        uses: actions/checkout@v2
+      - name: install Python
+        uses: actions/setup-python@v2
+      - name: load cached Python installation
+        id: cache
+        uses: actions/cache@v2
+        with:
+          path: ${{ env.pythonLocation }}
+          key: test-${{ runner.os }}-${{ env.pythonLocation }}-${{ hashFiles('pyproject.toml') }}
+      - name: install dependencies
+        run: pip install ".[testing]"
       - name: run tests with coverage
-        if: matrix.python-version == '3.x' && matrix.os == 'ubuntu-latest'
         run: pytest --numprocesses auto --cov . --cov-report xml:coverage.xml
+      - name: show coverage report
+        run: coverage report
       - name: upload coverage to Codecov
-        if: matrix.python-version == '3.x' && matrix.os == 'ubuntu-latest'
         uses: codecov/[email protected]
         with:
           token: ${{ secrets.CODECOV_TOKEN }}

diff --git a/pyproject.toml b/pyproject.toml
@@ -1,6 +1,51 @@
+[tool.poetry]
+name = 'coupledmodeldriver'
+version = '0.0.0'
+description = 'coupled model configuration generation'
+authors = ['Zach Burnett <[email protected]>']
+license = 'CC0-1.0'
+readme = 'README.md'
+repository = 'https://github.com/noaa-ocs-modeling/CoupledModelDriver.git'
+documentation = 'https://coupledmodeldriver.readthedocs.io'
+
 [build-system]
 requires = [
-    "dunamai",
-    "setuptools",
+    'poetry-core>=1.0.0',
+    'poetry-dynamic-versioning',
 ]
-build-backend = "setuptools.build_meta"
+build-backend = 'poetry.core.masonry.api'
+
+[tool.poetry-dynamic-versioning]
+enable = true
+
+[tool.poetry.dependencies]
+python = '^3.7'
+adcircpy = '>=1.1.2'
+file-read-backwards = '*'
+nemspy = '>=1.0.4'
+numpy = '*'
+pyproj = '*'
+typepigeon = '>=1.0.3'
+isort = { version = '*', optional = true }
+oitnb = { version = '*', optional = true }
+pooch = { version = '*', optional = true }
+pytest = { version = '*', optional = true }
+pytest-cov = { version = '*', optional = true }
+pytest-socket = { version = '*', optional = true }
+pytest-xdist = { version = '*', optional = true }
+wget = { version = '*', optional = true }
+m2r2 = { version = '*', optional = true }
+sphinx = { version = '*', optional = true }
+sphinx-rtd-theme = { version = '*', optional = true }
+sphinxcontrib-programoutput = { version = '*', optional = true }
+
+[tool.poetry.extras]
+testing = ['pooch', 'pytest', 'pytest-cov', 'pytest-socket', 'pytest-xdist', 'wget']
+development = ['isort', 'oitnb']
+documentation = ['m2r2', 'sphinx', 'sphinx-rtd-theme', 'sphinxcontrib-programoutput']
+
+[tool.poetry.scripts]
+initialize_adcirc = 'coupledmodeldriver.client.initialize_adcirc:main'
+generate_adcirc = 'coupledmodeldriver.client.generate_adcirc:main'
+check_completion = 'coupledmodeldriver.client.check_completion:main'
+unqueued_runs = 'coupledmodeldriver.client.unqueued_runs:main'
diff --git a/setup.cfg b/setup.cfg
diff --git a/setup.py b/setup.py
diff --git a/tests/data/reference/test_hera_adcirc/runs/unperturbed/fort.15 b/tests/data/reference/test_hera_adcirc/runs/unperturbed/fort.15
@@ -1,4 +1,4 @@
-created on 2022-02-22 12:57                                     ! RUNDES                              - 32 CHARACTER ALPHANUMERIC RUN DESCRIPTION
+created on 2022-04-21 08:35                                     ! RUNDES                              - 32 CHARACTER ALPHANUMERIC RUN DESCRIPTION
 Shinacock Inlet Coarse Grid                                     ! RUNID                               - 24 CHARACTER ALPANUMERIC RUN IDENTIFICATION
 1                                                               ! NFOVER                              - NONFATAL ERROR OVERRIDE OPTION
 1                                                               ! NABOUT                              - ABREVIATED OUTPUT OPTION PARAMETER

diff --git a/tests/data/reference/test_hera_adcirc_nems_atmesh_ww3data/runs/unperturbed/config.rc b/tests/data/reference/test_hera_adcirc_nems_atmesh_ww3data/runs/unperturbed/config.rc
@@ -1,4 +1,4 @@
-# `config.rc` generated with NEMSpy 1.0.5
+# `config.rc` generated with NEMSpy 1.0.8
  atm_dir: ../../../../input/forcings/ike
  atm_nam: wind_atm_fin_ch_time_vec.nc
  wav_dir: ../../../../input/forcings/ike

diff --git a/tests/data/reference/test_hera_adcirc_nems_atmesh_ww3data/runs/unperturbed/fort.15 b/tests/data/reference/test_hera_adcirc_nems_atmesh_ww3data/runs/unperturbed/fort.15
@@ -1,4 +1,4 @@
-created on 2022-02-22 12:57                                     ! RUNDES                              - 32 CHARACTER ALPHANUMERIC RUN DESCRIPTION
+created on 2022-04-21 08:35                                     ! RUNDES                              - 32 CHARACTER ALPHANUMERIC RUN DESCRIPTION
 Shinacock Inlet Coarse Grid                                     ! RUNID                               - 24 CHARACTER ALPANUMERIC RUN IDENTIFICATION
 1                                                               ! NFOVER                              - NONFATAL ERROR OVERRIDE OPTION
 1                                                               ! NABOUT                              - ABREVIATED OUTPUT OPTION PARAMETER

diff --git a/tests/data/reference/test_hera_adcirc_nems_atmesh_ww3data/runs/unperturbed/model_configure b/tests/data/reference/test_hera_adcirc_nems_atmesh_ww3data/runs/unperturbed/model_configure
@@ -1,4 +1,4 @@
-# `model_configure` generated with NEMSpy 1.0.5
+# `model_configure` generated with NEMSpy 1.0.8
 total_member:            1
 print_esmf:              .true.
 namelist:                atm_namelist.rc

diff --git a/tests/data/reference/test_hera_adcirc_nems_atmesh_ww3data/runs/unperturbed/nems.configure b/tests/data/reference/test_hera_adcirc_nems_atmesh_ww3data/runs/unperturbed/nems.configure
@@ -1,4 +1,4 @@
-# `nems.configure` generated with NEMSpy 1.0.5
+# `nems.configure` generated with NEMSpy 1.0.8
 # EARTH #
 EARTH_component_list: ATM WAV OCN
 EARTH_attributes::

diff --git a/tests/data/reference/test_hera_adcirc_tidal/runs/unperturbed/fort.15 b/tests/data/reference/test_hera_adcirc_tidal/runs/unperturbed/fort.15
@@ -1,4 +1,4 @@
-created on 2022-02-22 12:57                                     ! RUNDES                              - 32 CHARACTER ALPHANUMERIC RUN DESCRIPTION
+created on 2022-04-21 08:35                                     ! RUNDES                              - 32 CHARACTER ALPHANUMERIC RUN DESCRIPTION
 Shinacock Inlet Coarse Grid                                     ! RUNID                               - 24 CHARACTER ALPANUMERIC RUN IDENTIFICATION
 1                                                               ! NFOVER                              - NONFATAL ERROR OVERRIDE OPTION
 1                                                               ! NABOUT                              - ABREVIATED OUTPUT OPTION PARAMETER

diff --git a/tests/data/reference/test_hera_adcirc_tidal/spinup/fort.15 b/tests/data/reference/test_hera_adcirc_tidal/spinup/fort.15
@@ -1,4 +1,4 @@
-created on 2022-02-22 12:57                                     ! RUNDES                              - 32 CHARACTER ALPHANUMERIC RUN DESCRIPTION
+created on 2022-04-21 08:35                                     ! RUNDES                              - 32 CHARACTER ALPHANUMERIC RUN DESCRIPTION
 Shinacock Inlet Coarse Grid                                     ! RUNID                               - 24 CHARACTER ALPANUMERIC RUN IDENTIFICATION
 1                                                               ! NFOVER                              - NONFATAL ERROR OVERRIDE OPTION
 1                                                               ! NABOUT                              - ABREVIATED OUTPUT OPTION PARAMETER

diff --git a/...s/data/reference/test_hera_adcirc_tidal_besttrack_nems_ww3data/runs/unperturbed/config.rc b/...s/data/reference/test_hera_adcirc_tidal_besttrack_nems_ww3data/runs/unperturbed/config.rc
@@ -1,3 +1,3 @@
-# `config.rc` generated with NEMSpy 1.0.5
+# `config.rc` generated with NEMSpy 1.0.8
  wav_dir: ../../../../input/forcings/ike
  wav_nam: ww3.Constant.20151214_sxy_ike_date.nc
diff --git a/tests/data/reference/test_hera_adcirc_tidal_besttrack_nems_ww3data/runs/unperturbed/fort.15 b/tests/data/reference/test_hera_adcirc_tidal_besttrack_nems_ww3data/runs/unperturbed/fort.15
@@ -1,4 +1,4 @@
-created on 2022-02-22 12:57                                     ! RUNDES                              - 32 CHARACTER ALPHANUMERIC RUN DESCRIPTION
+created on 2022-04-21 08:35                                     ! RUNDES                              - 32 CHARACTER ALPHANUMERIC RUN DESCRIPTION
 Shinacock Inlet Coarse Grid                                     ! RUNID                               - 24 CHARACTER ALPANUMERIC RUN IDENTIFICATION
 1                                                               ! NFOVER                              - NONFATAL ERROR OVERRIDE OPTION
 1                                                               ! NABOUT                              - ABREVIATED OUTPUT OPTION PARAMETER