Merge pull request #345 from volkamerlab/dev

[2023.05.1-base] CI fixes and other housekeeping

.github/workflows/ci.yml

@@ -7,7 +7,7 @@ on:
   pull_request:
     branches:
       - "master"
-      - "base-ci-env-fix"
+      - "dev"
   schedule:
     # Run a cron job once weekly on Monday
     - cron: "0 3 * * 1"
@@ -73,25 +73,28 @@ jobs:
         run: |
           PYTEST_ARGS="--nbval-lax --current-env --dist loadscope --numprocesses 2"
 
-          # Ignore T019 under Windows, see https://github.com/volkamerlab/teachopencadd/issues/313
           PYTEST_IGNORE_T019="--ignore=teachopencadd/talktorials/T019_md_simulation/talktorial.ipynb"
+          PYTEST_IGNORE_T020="--ignore=teachopencadd/talktorials/T020_md_analysis/talktorial.ipynb"
 
-          # Temporarily ignored notebooks, see https://github.com/volkamerlab/teachopencadd/issues/303
-          PYTEST_IGNORE_T008="--ignore=teachopencadd/talktorials/T008_query_pdb/talktorial.ipynb"
+          IGNORE=""
 
-          if [ "$RUNNER_OS" != "Windows" ]; then
-            # Temporarily ignore T019
-            pytest $PYTEST_ARGS teachopencadd/talktorials/ $PYTEST_IGNORE_T008 $PYTEST_IGNORE_T019
-          else
-            pytest $PYTEST_ARGS teachopencadd/talktorials/ $PYTEST_IGNORE_T008 $PYTEST_IGNORE_T019
+          if [ "$RUNNER_OS" == "Windows" ]; then
+            # Ignore T019 under Windows, see https://github.com/volkamerlab/teachopencadd/issues/313
+            IGNORE="$IGNORE $PYTEST_IGNORE_T019"
           fi
 
+          if [ "$RUNNER_OS" == "macOS" ]; then
+            IGNORE="$IGNORE $PYTEST_IGNORE_T019"
+          fi
+
+          pytest $PYTEST_ARGS teachopencadd/talktorials/ $IGNORE
+
   format:
     name: Black
     runs-on: ubuntu-latest
     steps:
-      - uses: actions/checkout@v2
-      - uses: actions/setup-python@v2
+      - uses: actions/checkout@v3
+      - uses: actions/setup-python@v3
       - name: Install format dependencies
         run: python -m pip install black-nb shyaml
       - name: Run black-nb
@@ -102,8 +105,8 @@ jobs:
     name: READMEs
     runs-on: ubuntu-latest
     steps:
-      - uses: actions/checkout@v2
-      - uses: actions/setup-python@v2
+      - uses: actions/checkout@v3
+      - uses: actions/setup-python@v3
       - name: Install nbformat
         run: python -m pip install nbformat shyaml
       - name: Check READMEs are up-to-date

.github/workflows/docs.yml

@@ -61,20 +61,24 @@ jobs:
         shell: bash -l {0}
         run: |
           cd docs/_build/html
-          python -m http.server > /dev/null &2>1&
-          npx broken-link-checker http://localhost:8000/ --ordered --recursive \
-            --exclude "*.txt" \
-            --exclude "https://onlinelibrary.wiley.com/doi/full/10.1002/cmdc.200700139" \
-            --exclude "https://onlinelibrary.wiley.com/doi/10.1002/9783527806539.*" \
-            --exclude "https://towardsdatascience.com" \
-            --exclude "https://medium.com" \
-            --exclude "https://*.medium.com" \
-            --exclude "http[s]://quora.com" \
-            --exclude "http[s]://doi.org" \
-            --exclude "ftp://*" \
-            --exclude "http://localhost:8000" \
-            --exclude "https://pubs.acs.org/doi/10.1021/acs.jcim.9b00662" \
-            --exclude "https://pubs.acs.org/doi/abs/10.1021/bk-2021-1387.ch010"
+          npx linkinator . --verbosity error --recurse -r --retry-errors-jitter --timeout 10000 \
+            -s "/*.txt" \
+            -s "https://onlinelibrary.wiley.com/doi/full/10.1002/cmdc.200700139" \
+            -s "https://onlinelibrary.wiley.com/doi/10.1002/9783527806539.*" \
+            -s "https://towardsdatascience.com" \
+            -s "https://medium.com" \
+            -s "https://*.medium.com" \
+            -s "http[s]://quora.com" \
+            -s "http[s]://doi.org/*" \
+            -s "http[s]://pubs.acs.org/*" \
+            -s "ftp://*" \
+            -s "https://machinelearningmastery.com/*" \
+            -s "https://www.schrodinger.com/training/videos/*" \
+            -s "/*.mp4" \
+            -s "/*.pdf" \
+            -s "/*.png" \
+            -s "https://www.icoa.fr/pkidb/index.html" \
+            
 
       - name: Check 404s (README)
         uses: gaurav-nelson/github-action-markdown-link-check@v1

devtools/test_env.yml

@@ -29,7 +29,7 @@ dependencies:
   - pypdb
   - biopython<=1.77
   - biopandas
-  - rdkit==2021.09.5
+  - rdkit
   - openbabel
   - opencadd
   - biotite>=0.34.0

docs/contact.rst

@@ -5,5 +5,6 @@ Please contact us if you have questions or suggestions!
 
 - If you have questions regarding our Jupyter Notebooks, please `open an issue <https://github.com/volkamerlab/teachopencadd/issues>`_ on our GitHub repository.
 - If you have ideas for new topics, please fill out our `questionnaire <http://contribute.volkamerlab.org>`_.
+- If you have any further inquiries, please send us an `email <[email protected]>`_.
 
-We are looking forward to hearing from you!
+We are looking forward to hearing from you!

docs/external_dependencies.rst

@@ -13,7 +13,7 @@ Python packages
   - ``openbabel``: https://openbabel.org/
   - ``mdanalysis``: https://www.mdanalysis.org/
   - ``biopython``: https://biopython.org/
-  - ``biopandas``: http://rasbt.github.io/biopandas/
+  - ``biopandas``: https://biopandas.github.io/biopandas/
   - ``opencadd``: https://opencadd.readthedocs.io/en/latest/
   - ``plip``: https://github.com/pharmai/plip
   - ``openff``: https://github.com/openforcefield/openff-toolkit

docs/external_tutorials_collections.rst

@@ -7,8 +7,8 @@ Python programming
 The TeachOpenCADD platform is not a Python programming course from scratch but teaches how to solve tasks in cheminformatics and structural bioinformatics programmatically.
 If you wish to get started first with a Python programming introduction before diving into the TeachOpenCADD material, here are a few great resources to do so:
 
-- `AI in Medicine course <https://github.com/volkamerlab/ai_in_medicine>`_ by the `Volkamer Lab <https://volkamerlab.org/>`_ and `Ritter Lab <https://psychiatrie-psychotherapie.charite.de/metas/person/person/address_detail/ritter-7/>`_ at the Charité: Introduction to Python basics, Jupyter Notebook, and important data science packages such as ``pandas``, ``matplotlib``, and ``scikit-learn``
-- `Python for Chemists course <https://github.com/GDChCICTeam/python-for-chemists>`_ by the `GDCh/CIC <https://en.gdch.de/network-structures/divisions/computers-in-chemistry-cic.html>`_ team: Crash-course introduction to Python for natural scientists
+- `AI in Medicine course <https://github.com/volkamerlab/ai_in_medicine>`_ by the `Volkamer Lab <https://volkamerlab.org/>`_ and `Ritter Lab <https://psychiatrie-psychotherapie.charite.de/metas/person/person/address_detail/prof_dr_rer_nat_kerstin_ritter/>`_ at the Charité: Introduction to Python basics, Jupyter Notebook, and important data science packages such as ``pandas``, ``matplotlib``, and ``scikit-learn``
+- `Python for Chemists course <https://github.com/GDChCICTeam/python-for-chemists>`_ by the `GDCh/CIC <https://en.gdch.de/network-structures/gdch-structures/computers-in-chemistry-cic.html>`_ team: Crash-course introduction to Python for natural scientists
 - `MolSSI Education Resources <http://education.molssi.org/resources.html>`_ by `The Molecular Sciences Software Institute <https://molssi.org/>`_: Collection of tutorials on Python programming basics and data analysis but also more advanced material on software development and computational molecular science
 - `Core lessons <https://software-carpentry.org/lessons/>`_ by the `Software Carpentry <https://software-carpentry.org/>`_: Introduction to Python, Git, command line interfaces and more
 - `Best practices for Python, Git and Jupyter <https://zenodo.org/record/4630714>`_, a slide deck used in the introduction of our CADD Block course 2021, part of the Master's degree in Bioinformatics curriculum at the Freie Universität (FU) Berlin.