Fix dead links

.github/workflows/docs.yml

@@ -72,6 +72,13 @@ jobs:
             -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

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 <teachopencadd@lists.cs.uni-saarland.de>`_.
 
-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.

teachopencadd/talktorials/T011_query_online_api_webservices/talktorial.ipynb

@@ -227,7 +227,7 @@
      "name": "stdout",
      "output_type": "stream",
      "text": [
-      "xName,Manning Name,HGNC Name,Kinase Name,Group,Family,SubFamily,UniprotID\n",
+      "xName,Manning Name,HGNC Name,Kinase Name,Group,Family,SubFamily,UniprotID\n",
       "ABL1,ABL,ABL1,Tyrosine-protein kinase ABL1,TK,Abl,,P00519\n",
       "ACK,ACK,TNK2,Activated CDC42 kinase 1,TK,Ack,,Q07912\n",
       "ACTR2,ACTR2,ACVR2A,Activin receptor type-2A,TKL,STKR,STKR2,P27037\n",
@@ -439,10 +439,11 @@
    ]
   },
   {
+   "attachments": {},
    "cell_type": "markdown",
    "metadata": {},
    "source": [
-    "One note about file downloads. The method above downloads the whole file into memory, which can be a problem for very big files. If you intend to download a very large file, you can push it to disk directly using [streaming requests](https://requests.readthedocs.io/en/master/user/advanced/#streaming-requests) and [raw responses](https://2.python-requests.org/en/master/user/quickstart/#raw-response-content). As an example, let's pretend this [1MB video](https://archive.org/download/SlowMotionFlame/slomoflame_512kb.mp4) is _too big to fit in memory_:"
+    "One note about file downloads. The method above downloads the whole file into memory, which can be a problem for very big files. If you intend to download a very large file, you can push it to disk directly using [streaming requests](https://requests.readthedocs.io/en/master/user/advanced/#streaming-requests) and [raw responses](https://docs.python-requests.org/en/v1.1.0/user/quickstart/?highlight=raw%20response#raw-response-content). As an example, let's pretend this [1MB video](https://archive.org/download/SlowMotionFlame/slomoflame_512kb.mp4) is _too big to fit in memory_:"
    ]
   },
   {
@@ -1771,6 +1772,7 @@
    ]
   },
   {
+   "attachments": {},
    "cell_type": "markdown",
    "metadata": {},
    "source": [
@@ -1782,8 +1784,8 @@
     "\n",
     "Unfortunately, there is too much material to cover about web APIs in a single lesson. For example, how do you _send_ or _upload_ contents from Python? Can you submit forms? If you are interested in knowing more, the `requests` [documentation](https://requests.readthedocs.io/) should be your go-to resource. Some interesting parts include:\n",
     "\n",
-    "* [Submitting forms with POST requests](https://2.python-requests.org/en/master/user/quickstart/#more-complicated-post-requests)\n",
-    "* [User authentication](https://2.python-requests.org/en/master/user/authentication/#basic-authentication)"
+    "* [Submitting forms with POST requests](https://docs.python-requests.org/en/v1.1.0/user/quickstart/#more-complicated-post-requests)\n",
+    "* [User authentication](https://docs.python-requests.org/en/v1.1.0/user/authentication/#basic-authentication)"
    ]
   },
   {
@@ -1814,7 +1816,7 @@
    "name": "python",
    "nbconvert_exporter": "python",
    "pygments_lexer": "ipython3",
-   "version": "3.9.7"
+   "version": "3.7.8"
   },
   "toc-autonumbering": true,
   "widgets": {