From d4112b8fac08b4f68d1ef99e42d7569c6d77cced Mon Sep 17 00:00:00 2001 From: dominiquesydow Date: Wed, 29 Sep 2021 10:48:36 +0200 Subject: [PATCH 1/8] Add numpy to environment --- devtools/test_env.yml | 1 + 1 file changed, 1 insertion(+) diff --git a/devtools/test_env.yml b/devtools/test_env.yml index 5940ba63..6065a550 100644 --- a/devtools/test_env.yml +++ b/devtools/test_env.yml @@ -6,6 +6,7 @@ dependencies: - pip - jupyter - jupyterlab>=3 + - numpy - rdkit>=2021.03 - scikit-learn - biopandas From dd0a4e2037e9dd43fd21568e0c95dba32711d5a7 Mon Sep 17 00:00:00 2001 From: dominiquesydow Date: Wed, 29 Sep 2021 13:37:24 +0200 Subject: [PATCH 2/8] CI: Increase Python version 3.6 > 3.7 --- .github/workflows/ci.yml | 6 +++--- 1 file changed, 3 insertions(+), 3 deletions(-) diff --git a/.github/workflows/ci.yml b/.github/workflows/ci.yml index d1b84f8e..44ead1a0 100644 --- a/.github/workflows/ci.yml +++ b/.github/workflows/ci.yml @@ -22,13 +22,13 @@ jobs: matrix: cfg: - os: ubuntu-latest - python-version: "3.6" + python-version: "3.7" - os: ubuntu-latest python-version: "3.9" - os: macos-latest - python-version: "3.6" + python-version: "3.7" - os: windows-latest - python-version: "3.6" + python-version: "3.7" env: PYVER: ${{ matrix.cfg.python-version }} From b8c0b263f32f3c0298d138b464df2c7342999590 Mon Sep 17 00:00:00 2001 From: dominiquesydow Date: Wed, 29 Sep 2021 13:37:48 +0200 Subject: [PATCH 3/8] Env: Require Python >=3.7 --- devtools/test_env.yml | 2 +- 1 file changed, 1 insertion(+), 1 deletion(-) diff --git a/devtools/test_env.yml b/devtools/test_env.yml index 6065a550..ae8384d9 100644 --- a/devtools/test_env.yml +++ b/devtools/test_env.yml @@ -2,7 +2,7 @@ channels: - conda-forge dependencies: - - python>=3.6 + - python>=3.7 - pip - jupyter - jupyterlab>=3 From b26a0b2df99b4f4312941f429fdf2b001b500f6e Mon Sep 17 00:00:00 2001 From: Unknown Date: Wed, 29 Sep 2021 14:18:10 +0200 Subject: [PATCH 4/8] CI: Build conda package with Python 3.7 (not 3.6) --- .github/workflows/ci.yml | 2 +- 1 file changed, 1 insertion(+), 1 deletion(-) diff --git a/.github/workflows/ci.yml b/.github/workflows/ci.yml index 44ead1a0..0b46a8d4 100644 --- a/.github/workflows/ci.yml +++ b/.github/workflows/ci.yml @@ -121,7 +121,7 @@ jobs: - uses: conda-incubator/setup-miniconda@v2 with: - python-version: 3.6 + python-version: 3.7 channel-priority: true auto-activate-base: true channels: conda-forge,defaults From 6b4a4b139d12da9738491fae1ee11c7ad3d17859 Mon Sep 17 00:00:00 2001 From: Unknown Date: Wed, 29 Sep 2021 14:20:30 +0200 Subject: [PATCH 5/8] CI: Include T019 under Windows --- .github/workflows/ci.yml | 6 +----- 1 file changed, 1 insertion(+), 5 deletions(-) diff --git a/.github/workflows/ci.yml b/.github/workflows/ci.yml index 0b46a8d4..6d59c634 100644 --- a/.github/workflows/ci.yml +++ b/.github/workflows/ci.yml @@ -72,11 +72,7 @@ jobs: shell: bash -l {0} run: | PYTEST_ARGS="--nbval-lax --current-env --dist loadscope --numprocesses 2" - if [ "$RUNNER_OS" != "Windows" ]; then - pytest $PYTEST_ARGS teachopencadd/talktorials/T*/talktorial.ipynb - else - pytest $PYTEST_ARGS teachopencadd/talktorials/ --ignore-glob=teachopencadd/talktorials/T019* - fi + pytest $PYTEST_ARGS teachopencadd/talktorials/T*/talktorial.ipynb format: name: Black From 9736c10b69435b1dd3aad709a8b1dfce5d60a45d Mon Sep 17 00:00:00 2001 From: dominiquesydow Date: Mon, 4 Oct 2021 08:21:39 +0200 Subject: [PATCH 6/8] CI: Revert back to not testing T019 under Windows --- .github/workflows/ci.yml | 6 +++++- 1 file changed, 5 insertions(+), 1 deletion(-) diff --git a/.github/workflows/ci.yml b/.github/workflows/ci.yml index 6d59c634..0b46a8d4 100644 --- a/.github/workflows/ci.yml +++ b/.github/workflows/ci.yml @@ -72,7 +72,11 @@ jobs: shell: bash -l {0} run: | PYTEST_ARGS="--nbval-lax --current-env --dist loadscope --numprocesses 2" - pytest $PYTEST_ARGS teachopencadd/talktorials/T*/talktorial.ipynb + if [ "$RUNNER_OS" != "Windows" ]; then + pytest $PYTEST_ARGS teachopencadd/talktorials/T*/talktorial.ipynb + else + pytest $PYTEST_ARGS teachopencadd/talktorials/ --ignore-glob=teachopencadd/talktorials/T019* + fi format: name: Black From 2429797923cca14c2f640d34c220a0af56b489ff Mon Sep 17 00:00:00 2001 From: Unknown Date: Mon, 4 Oct 2021 08:43:15 +0200 Subject: [PATCH 7/8] Stream-line both environments (test, users) --- devtools/other-conda-envs/users_env.yml | 4 +++- devtools/test_env.yml | 1 + 2 files changed, 4 insertions(+), 1 deletion(-) diff --git a/devtools/other-conda-envs/users_env.yml b/devtools/other-conda-envs/users_env.yml index f1c9b874..ed51cc35 100644 --- a/devtools/other-conda-envs/users_env.yml +++ b/devtools/other-conda-envs/users_env.yml @@ -2,10 +2,12 @@ name: teachopencadd channels: - conda-forge dependencies: - - python>=3.6 + - python>=3.7 - pip - jupyter - jupyterlab>=3 + # Explicitly add numpy because of https://github.com/volkamerlab/teachopencadd/issues/150 + - numpy - rdkit>=2021.03 - scikit-learn - biopandas diff --git a/devtools/test_env.yml b/devtools/test_env.yml index ae8384d9..b8a71f1c 100644 --- a/devtools/test_env.yml +++ b/devtools/test_env.yml @@ -6,6 +6,7 @@ dependencies: - pip - jupyter - jupyterlab>=3 + # Explicitly add numpy because of https://github.com/volkamerlab/teachopencadd/issues/150 - numpy - rdkit>=2021.03 - scikit-learn From a579092e3a63289982cbf828513f720a54c10c03 Mon Sep 17 00:00:00 2001 From: Unknown Date: Mon, 4 Oct 2021 09:35:50 +0200 Subject: [PATCH 8/8] Env workaround: Add jsonschema pinned to <4.0.0 to fix bravado errors --- devtools/other-conda-envs/users_env.yml | 2 ++ devtools/test_env.yml | 2 ++ 2 files changed, 4 insertions(+) diff --git a/devtools/other-conda-envs/users_env.yml b/devtools/other-conda-envs/users_env.yml index ed51cc35..92d2e9f0 100644 --- a/devtools/other-conda-envs/users_env.yml +++ b/devtools/other-conda-envs/users_env.yml @@ -20,6 +20,8 @@ dependencies: - openbabel - tqdm - lxml + # Remove jsonschema once this issue is fixed: https://github.com/Yelp/bravado/issues/478 + - jsonschema<4.0.0 - bravado - beautifulsoup4 - ipywidgets>=7.5 diff --git a/devtools/test_env.yml b/devtools/test_env.yml index b8a71f1c..13921956 100644 --- a/devtools/test_env.yml +++ b/devtools/test_env.yml @@ -20,6 +20,8 @@ dependencies: - openbabel - tqdm - lxml + # Remove jsonschema once this issue is fixed: https://github.com/Yelp/bravado/issues/478 + - jsonschema<4.0.0 - bravado - beautifulsoup4 - ipywidgets>=7.5