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Fix docs CI after version updates (#23)
* update actions versions * check what line is causing the error * reenable without tab * remove caching * install docs requirements * source common * activate bioconda * init conda * readd other activate * update deprecated status_iterator * update extlinks conf for new sphinx version * remove jquery * improve error messages * fix typo * fix a few minor errors
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‎.github/workflows/docs.yml

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@@ -15,32 +15,26 @@ jobs:
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build-and-test:
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runs-on: "ubuntu-latest"
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steps:
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- uses: actions/checkout@v3
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- uses: actions/checkout@v4
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- name: set path
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run: echo "/opt/mambaforge/bin" >> $GITHUB_PATH
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- name: Fetch conda install script
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run: |
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wget https://raw.githubusercontent.com/bioconda/bioconda-common/bulk/{common,install-and-set-up-conda,configure-conda}.sh
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- name: Restore cache
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id: cache
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uses: actions/cache@v3
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with:
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path: /opt/mambaforge
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key: ${{ runner.os }}--bulk--${{ hashFiles('install-and-set-up-conda.sh', 'common.sh', 'configure-conda.sh') }}
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wget https://raw.githubusercontent.com/bioconda/bioconda-common/master/{common,install-and-set-up-conda,configure-conda}.sh
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- name: Set up bioconda-utils
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if: steps.cache.outputs.cache-hit != 'true'
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run: bash install-and-set-up-conda.sh
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30+
- name: Install docs requirements
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run: |
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source common.sh
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eval "$(conda shell.bash hook)"
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conda activate bioconda
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conda install -y --file https://raw.githubusercontent.com/bioconda/bioconda-utils/$BIOCONDA_UTILS_TAG/bioconda_utils/bioconda_utils-requirements-docs.txt
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# This script can be used to reconfigure conda to use the right channel setup.
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# This has to be done after the cache is restored, because
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# the channel setup is not cached as it resides in the home directory.
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# We could use a system-wide (and therefore cached) channel setup,
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# but mamba does not support that at the time of implementation
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# (it ignores settings made with --system).
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- name: Configure conda
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run: bash configure-conda.sh
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@@ -74,7 +68,7 @@ jobs:
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# Upload the built docs as an artifact for inspection (even on PRs). This
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# will show up in the Actions web interface.
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- name: push artifact
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uses: actions/upload-artifact@v3
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uses: actions/upload-artifact@v4
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with:
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name: doc
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path: docs.tar

‎Makefile

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@@ -9,7 +9,7 @@ BUILDDIR = build
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# User-friendly check for sphinx-build
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ifeq ($(shell which $(SPHINXBUILD) >/dev/null 2>&1; echo $$?), 1)
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$(error The '$(SPHINXBUILD)' command was not found. Make sure you have Sphinx installed, then set the SPHINXBUILD environment variable to point to the full path of the '$(SPHINXBUILD)' executable. Alternatively you can add the directory with the executable to your PATH. If you don\'t have Sphinx installed, grab it from http://sphinx-doc.org/)
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$(error The '$(SPHINXBUILD)' command was not found. Make sure you have Sphinx installed, then set the SPHINXBUILD environment variable to point to the full path of the '$(SPHINXBUILD)' executable. Alternatively you can add the directory with the executable to your PATH. If you don\'t have Sphinx installed, grab it from http://sphinx-doc.org/)
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endif
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# Internal variables.

‎source/_ext/bioconda_sphinx_ext.py

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Original file line numberDiff line numberDiff line change
@@ -37,7 +37,7 @@
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from sphinx.environment import BuildEnvironment
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from sphinx.roles import XRefRole
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from sphinx.util import logging as sphinx_logging
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from sphinx.util import status_iterator
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from sphinx.util.display import status_iterator
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from sphinx.util.docfields import Field, GroupedField
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from sphinx.util.nodes import make_refnode
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from sphinx.util.parallel import ParallelTasks, parallel_available, make_chunks

‎source/conf.py

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Original file line numberDiff line numberDiff line change
@@ -308,14 +308,14 @@ def setup(app):
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# We are using the `extlinks` extension to render links for identifiers:
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extlinks = {
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"biotools": ("https://bio.tools/%s", ""),
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"doi": ("https://doi.org/%s", ""),
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"debian": ("https://tracker.debian.org/pkg/%s", ""),
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"pmid": ("https://www.ncbi.nlm.nih.gov/pubmed/%s", ""),
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"rrid": ("https://scicrunch.org/resolver/%s", ""),
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"usegalaxy-eu": ("https://usegalaxy.eu/?tool_id=%s", ""),
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"usegalaxy-org": ("https://usegalaxy.org/?tool_id=%s", ""),
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"usegalaxy-org.au": ("https://usegalaxy.org.au/?tool_id=%s", ""),
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"biotools": ("https://bio.tools/%s", "%s"),
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"doi": ("https://doi.org/%s", "%s"),
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"debian": ("https://tracker.debian.org/pkg/%s", "%s"),
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"pmid": ("https://www.ncbi.nlm.nih.gov/pubmed/%s", "%s"),
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"rrid": ("https://scicrunch.org/resolver/%s", "%s"),
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"usegalaxy-eu": ("https://usegalaxy.eu/?tool_id=%s", "%s"),
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"usegalaxy-org": ("https://usegalaxy.org/?tool_id=%s", "%s"),
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"usegalaxy-org.au": ("https://usegalaxy.org.au/?tool_id=%s", "%s"),
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}
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# add document name before automatic section title reference

‎source/templates/dashboard.html

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Original file line numberDiff line numberDiff line change
@@ -2,10 +2,9 @@
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<div style="width: 100%" id="package_plot"></div>
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<script>
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window.onload = function () {
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// Download download plot data
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$.get("https://raw.githubusercontent.com/bioconda/bioconda-stats/data/package-downloads/anaconda.org/bioconda/channel.tsv", function (bioconda_data) {
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window.onload = async function () {
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function buildDownloadsPlot(bioconda_data) {
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let spec = {
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"$schema": "https://vega.github.io/schema/vega-lite/v5.json",
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"description": "Total bioconda downloads.",
@@ -52,11 +51,21 @@
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};
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vegaEmbed('#download_plot', spec);
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});
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}
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// Download download plot data
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$.get("https://raw.githubusercontent.com/bioconda/bioconda-stats/data/package-downloads/anaconda.org/bioconda/packages.tsv", function (package_data) {
57+
try {
58+
const bioconda_resp = await fetch("https://raw.githubusercontent.com/bioconda/bioconda-stats/data/package-downloads/anaconda.org/bioconda/channel.tsv")
59+
if (!bioconda_resp.ok) {
60+
throw new Error(`Fetching failed with HTTP code ${bioconda_resp.status}.`);
61+
}
62+
const bioconda_data = await bioconda_resp.text();
63+
buildDownloadsPlot(bioconda_data);
64+
} catch (err) {
65+
console.error("An error occurred while building channel downloads plot: ", err)
66+
}
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68+
function buildTopPackagesPlot(package_data) {
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let package_spec = {
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"$schema": "https://vega.github.io/schema/vega-lite/v5.json",
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"description": "Top downloaded packages.",
@@ -85,6 +94,20 @@
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};
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vegaEmbed('#package_plot', package_spec);
88-
});
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};
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99+
100+
// Download package plot data
101+
try {
102+
const package_resp = await fetch("https://raw.githubusercontent.com/bioconda/bioconda-stats/data/package-downloads/anaconda.org/bioconda/packages.tsv")
103+
if (!package_resp.ok) {
104+
throw new Error(`Fetching failed with HTTP code ${package_resp.status}.`);
105+
}
106+
const package_data = await package_resp.text();
107+
buildTopPackagesPlot(package_data);
108+
} catch (err) {
109+
console.error("An error occurred while building top packages plot: ", err)
110+
}
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}
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</script>

‎source/templates/layout.html

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@@ -23,7 +23,7 @@
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<meta name="msapplication-TileColor" content="#ffffff">
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<meta name="msapplication-TileImage" content="{{pathto('_static/ms-icon-144x144.png', 1)}}">
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<link rel="manifest" href="/manifest.json">
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<link rel="manifest" href="{{pathto('_static/manifest.json', 1)}}">
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<meta name="theme-color" content="#ffffff">
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{{ super() }}
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{% endblock %}
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3838
if (elem != null) {
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// Get the closest "details" element and open it
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closest = elem.closest("details");
41-
closest.open = true;
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if (closest) closest.open = true;
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}
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</script>
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‎source/templates/package_dashboard.html

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@@ -3,23 +3,49 @@
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<script>
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window.onload = async function() {
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$.get(`https://raw.githubusercontent.com/bioconda/bioconda-plots/main/resources/cdf.vl.json`, function( data ) {
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let spec = JSON.parse(data);
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$.get(`https://raw.githubusercontent.com/bioconda/bioconda-plots/main/plots/cdf.json`, function( plot_data ) {
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$.get(`https://raw.githubusercontent.com/bioconda/bioconda-plots/main/plots/${package}/cdf.json`, function( single_point ) {
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spec.data.values = JSON.parse(plot_data);
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spec.data.values.push(JSON.parse(single_point).pop());
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vegaEmbed('#cdf_plot', spec);
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});
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});
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});
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$.get(`https://raw.githubusercontent.com/bioconda/bioconda-plots/main/resources/versions.vl.json`, function( data ) {
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let spec = JSON.parse(data);
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$.get(`https://raw.githubusercontent.com/bioconda/bioconda-plots/main/plots/${package}/versions.json`, function( plot_data ) {
20-
spec.data.values = JSON.parse(plot_data);
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vegaEmbed('#download_plot', spec);
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});
23-
});
6+
7+
// Build cdf plot
8+
try {
9+
const cdf_spec_resp = await fetch("https://raw.githubusercontent.com/bioconda/bioconda-plots/main/resources/cdf.vl.json")
10+
if (!cdf_spec_resp.ok) {
11+
throw new Error(`Fetching failed with HTTP code ${cdf_spec_resp.status}.`);
12+
}
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const cdf_spec = await cdf_spec_resp.json();
14+
const cdf_data_resp = await fetch("https://raw.githubusercontent.com/bioconda/bioconda-plots/main/plots/cdf.json")
15+
if (!cdf_data_resp.ok) {
16+
throw new Error(`Fetching failed with HTTP code ${cdf_data_resp.status}.`);
17+
}
18+
const cdf_plot_data = await cdf_data_resp.json();
19+
const point_data_resp = await fetch(`https://raw.githubusercontent.com/bioconda/bioconda-plots/main/plots/${package}/cdf.json`)
20+
if (!point_data_resp.ok) {
21+
throw new Error(`Fetching failed with HTTP code ${point_data_resp.status}.`);
22+
}
23+
const single_point = await point_data_resp.json();
24+
25+
cdf_spec.data.values = cdf_plot_data;
26+
cdf_spec.data.values.push(single_point.pop());
27+
vegaEmbed('#cdf_plot', cdf_spec);
28+
} catch (err) {
29+
console.error("An error occurred while building CDF plot: ", err)
30+
}
31+
32+
// Build download plot
33+
try {
34+
const spec_resp = await fetch("https://raw.githubusercontent.com/bioconda/bioconda-plots/main/resources/versions.vl.json")
35+
if (!spec_resp.ok) {
36+
throw new Error(`Fetching failed with HTTP code ${spec_resp.status}.`);
37+
}
38+
const spec = await spec_resp.json();
39+
const version_data_resp = await fetch(`https://raw.githubusercontent.com/bioconda/bioconda-plots/main/plots/${package}/versions.json`)
40+
if (!version_data_resp.ok) {
41+
throw new Error(`Fetching failed with HTTP code ${version_data_resp.status}.`);
42+
}
43+
const plot_data = await version_data_resp.json();
44+
spec.data.values = plot_data;
45+
vegaEmbed('#download_plot', spec);
46+
} catch (err) {
47+
console.error("An error occurred while building downloads plot: ", err)
48+
}
49+
2450
}
2551
</script>

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