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Fix T008 under windows #229

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merged 5 commits into from
Apr 21, 2022
Merged

Fix T008 under windows #229

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0ceae4b
sleep when querying per year
schallerdavid Apr 20, 2022
27f6b66
add more sleep time
schallerdavid Apr 20, 2022
27a01d7
exclude failing links
schallerdavid Apr 20, 2022
8a46443
disable link check for two lines
schallerdavid Apr 20, 2022
872f154
disable link check for third line
schallerdavid Apr 20, 2022
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5 changes: 3 additions & 2 deletions .github/workflows/docs.yml
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Original file line number Diff line number Diff line change
Expand Up @@ -73,8 +73,9 @@ jobs:
--exclude "http[s]://quora.com" \
--exclude "http[s]://doi.org" \
--exclude "ftp://*" \
--exclude "http://localhost:8000"

--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"

- name: Check 404s (README)
uses: gaurav-nelson/github-action-markdown-link-check@v1
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3 changes: 3 additions & 0 deletions README.md
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Expand Up @@ -62,6 +62,7 @@ If you'd like to execute the provided notebooks, we offer two possibilities:

## TeachOpenCADD KNIME workflows

<!-- markdown-link-check-disable-next-line -->
[![DOI](https://img.shields.io/badge/DOI-10.1021%2Facs.jcim.9b00662-blue.svg)](https://pubs.acs.org/doi/10.1021/acs.jcim.9b00662)
[![DOI](https://zenodo.org/badge/DOI/10.5281/zenodo.3626897.svg)](https://doi.org/10.5281/zenodo.3626897)
[![KNIME Hub](https://img.shields.io/badge/KNIME%20Hub-TeachOpenCADD--KNIME-yellow.svg)](https://hub.knime.com/volkamerlab/spaces/Public/latest/TeachOpenCADD/TeachOpenCADD)
Expand Down Expand Up @@ -110,7 +111,9 @@ To view a copy of this license, visit http://creativecommons.org/licenses/by/4.0
If you make use of the TeachOpenCADD material in scientific publications, please cite our respective articles:

- [TeachOpenCADD Jupyter Notebooks: Talktorials T001-T010](https://jcheminf.biomedcentral.com/articles/10.1186/s13321-019-0351-x)
<!-- markdown-link-check-disable-next-line -->
- [TeachOpenCADD KNIME workflows](https://pubs.acs.org/doi/10.1021/acs.jcim.9b00662)
<!-- markdown-link-check-disable-next-line -->
- [How to use the TeachOpenCADD material for teaching?](https://pubs.acs.org/doi/abs/10.1021/bk-2021-1387.ch010)

It will help measure the impact of the TeachOpenCADD platform and future funding!
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11 changes: 9 additions & 2 deletions teachopencadd/talktorials/T008_query_pdb/talktorial.ipynb
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Expand Up @@ -292,7 +292,9 @@
" \"and\",\n",
" )\n",
" # Count matching structures and add to list\n",
" n_structures.append(rcsb.count(query))"
" n_structures.append(rcsb.count(query))\n",
" # wait shortly to not overload the API\n",
" time.sleep(0.1)"
]
},
{
Expand Down Expand Up @@ -439,16 +441,21 @@
],
"source": [
"print(f\"Number of structures with UniProt ID {uniprot_id}: {rcsb.count(query_by_uniprot_id)}\")\n",
"time.sleep(0.1) # wait shortly to not overload the API\n",
"print(\n",
" f\"Number of structures deposited before {before_deposition_date}: {rcsb.count(query_by_deposition_date)}\"\n",
")\n",
"time.sleep(0.1)\n",
"print(\n",
" f\"Number of structures resolved by {experimental_method}: {rcsb.count(query_by_experimental_method)}\"\n",
")\n",
"time.sleep(0.1)\n",
"print(\n",
" f\"Number of structures with resolution less than or equal to {max_resolution}: {rcsb.count(query_by_resolution)}\"\n",
")\n",
"time.sleep(0.1)\n",
"print(f\"Number of structures with only {n_chains} chain: {rcsb.count(query_by_polymer_count)}\")\n",
"time.sleep(0.1)\n",
"print(\n",
" f\"Number of structures with ligand of more than or equal to {min_ligand_molecular_weight} Da: {rcsb.count(query_by_ligand_mw)}\"\n",
")"
Expand Down Expand Up @@ -1564,7 +1571,7 @@
"name": "python",
"nbconvert_exporter": "python",
"pygments_lexer": "ipython3",
"version": "3.9.6"
"version": "3.9.12"
},
"toc-autonumbering": true,
"widgets": {
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