Skip to content

Commit

Permalink
fix(ci): don't try to push docs on master push (#199)
Browse files Browse the repository at this point in the history
* fix(ci): don't try to push docs on master push

* fix(ci): don't try to commit docs on master push

* chore(ci): fix names

* fix(ci): yaml syntax

* fix(ci): run at correct times

* fix(ci): ensure running on newly opened PRs

* fix(ci): run tests on all branches

* fix(ci): remove trailing ' preventing run

* Apply automatic documentation changes
  • Loading branch information
Avantol13 authored Oct 16, 2023
1 parent 475d45c commit 0e0bf46
Show file tree
Hide file tree
Showing 9 changed files with 64 additions and 55 deletions.
52 changes: 3 additions & 49 deletions .github/workflows/ci.yaml
Original file line number Diff line number Diff line change
@@ -1,9 +1,10 @@
name: CI

on:
# run on pushed commits to master and on new commits on pull requests
push:
pull_request:
types: [opened, reopened]
types: [opened, synchronize]

jobs:
Security:
Expand All @@ -16,51 +17,4 @@ jobs:
name: Python Unit Test
uses: uc-cdis/.github/.github/workflows/python_unit_test.yaml@master
with:
python-version: '3.9'

build_docs:
runs-on: ubuntu-latest

steps:
- uses: actions/checkout@v2
with:
ref: ${{github.event.pull_request.head.ref}}
repository: ${{github.event.pull_request.head.repo.full_name}}
- name: Set up Python 3.9
uses: actions/setup-python@v1
with:
python-version: 3.9
- uses: actions/cache@preview
with:
path: ~/.cache/pypoetry/virtualenvs
key: ${{ runner.os }}-poetry-${{ hashFiles(format('{0}{1}', github.workspace, '/poetry.lock')) }}
restore-keys: |
${{ runner.os }}-poetry-
- name: Install dependencies
run: |
pip install poetry
poetry config virtualenvs.create false
poetry install -vv --all-extras --no-interaction
poetry show -vv
# install sphinx from PyPI (as of 03/16/21 python3-sphinx is broken)
# sudo apt-get install python3-sphinx
pip install sphinx
pip uninstall -y asyncio
pip list
cd
- name: Build docs
run: |
sphinx-build --version
export PYTHONPATH="${PYTHONPATH}:${{ env.pythonLocation }}/lib/python3.9/site-packages"
cd docs
poetry run make html
cd ..
- uses: stefanzweifel/[email protected]
with:
commit_message: Apply automatic documentation changes

# Optional name of the branch the commit should be pushed to
# Required if Action is used in Workflow listening to the `pull_request` event
branch: ${{ github.head_ref }}
python-version: '3.9'
54 changes: 54 additions & 0 deletions .github/workflows/docs.yaml
Original file line number Diff line number Diff line change
@@ -0,0 +1,54 @@
name: Docs

on:
# DON'T run on pushed commits to master, ONLY on new commits on pull requests
pull_request:
types: [opened, synchronize]

jobs:
build_docs:
runs-on: ubuntu-latest

steps:
- uses: actions/checkout@v2
with:
ref: ${{github.event.pull_request.head.ref}}
repository: ${{github.event.pull_request.head.repo.full_name}}
- name: Set up Python 3.9
uses: actions/setup-python@v1
with:
python-version: 3.9
- uses: actions/cache@preview
with:
path: ~/.cache/pypoetry/virtualenvs
key: ${{ runner.os }}-poetry-${{ hashFiles(format('{0}{1}', github.workspace, '/poetry.lock')) }}
restore-keys: |
${{ runner.os }}-poetry-
- name: Install dependencies
run: |
pip install poetry
poetry config virtualenvs.create false
poetry install -vv --all-extras --no-interaction
poetry show -vv
# install sphinx from PyPI (as of 03/16/21 python3-sphinx is broken)
# sudo apt-get install python3-sphinx
pip install sphinx
pip uninstall -y asyncio
pip list
cd
- name: Build docs
run: |
sphinx-build --version
export PYTHONPATH="${PYTHONPATH}:${{ env.pythonLocation }}/lib/python3.9/site-packages"
cd docs
poetry run make html
cd ..
- uses: stefanzweifel/[email protected]
with:
commit_message: Apply automatic documentation changes

# Optional name of the branch the commit should be pushed to
# Required if Action is used in Workflow listening to the `pull_request` event
branch: ${{ github.head_ref }}
7 changes: 4 additions & 3 deletions .github/workflows/lint.yaml
Original file line number Diff line number Diff line change
@@ -1,5 +1,6 @@
on:
pull_request
pull_request:
types: [opened, synchronize]
issue_comment:
types: [created, edited]

Expand All @@ -12,5 +13,5 @@ jobs:
steps:
- uses: actions/checkout@master
- uses: uc-cdis/wool@master
env:
GITHUB_TOKEN: ${{ secrets.GITHUB_TOKEN }}
env:
GITHUB_TOKEN: ${{ secrets.GITHUB_TOKEN }}
Binary file modified docs/_build/doctrees/environment.pickle
Binary file not shown.
Binary file modified docs/_build/doctrees/tools/indexing.doctree
Binary file not shown.
Binary file modified docs/_build/doctrees/tools/metadata.doctree
Binary file not shown.
2 changes: 1 addition & 1 deletion docs/_build/html/searchindex.js

Large diffs are not rendered by default.

2 changes: 1 addition & 1 deletion docs/_build/html/tools/indexing.html
Original file line number Diff line number Diff line change
Expand Up @@ -380,7 +380,7 @@ <h1>Indexing Tools<a class="headerlink" href="#indexing-tools" title="Link to th

<dl class="py function">
<dt class="sig sig-object py" id="gen3.tools.indexing.verify_manifest.async_verify_object_manifest">
<em class="property"><span class="k"><span class="pre">async</span></span><span class="w"> </span></em><span class="sig-prename descclassname"><span class="pre">gen3.tools.indexing.verify_manifest.</span></span><span class="sig-name descname"><span class="pre">async_verify_object_manifest</span></span><span class="sig-paren">(</span><em class="sig-param"><span class="n"><span class="pre">commons_url</span></span></em>, <em class="sig-param"><span class="n"><span class="pre">manifest_file</span></span></em>, <em class="sig-param"><span class="n"><span class="pre">max_concurrent_requests=24</span></span></em>, <em class="sig-param"><span class="n"><span class="pre">manifest_row_parsers={'acl':</span> <span class="pre">&lt;function</span> <span class="pre">_get_acl_from_row&gt;</span></span></em>, <em class="sig-param"><span class="n"><span class="pre">'authz':</span> <span class="pre">&lt;function</span> <span class="pre">_get_authz_from_row&gt;</span></span></em>, <em class="sig-param"><span class="n"><span class="pre">'file_name':</span> <span class="pre">&lt;function</span> <span class="pre">_get_file_name_from_row&gt;</span></span></em>, <em class="sig-param"><span class="n"><span class="pre">'file_size':</span> <span class="pre">&lt;function</span> <span class="pre">_get_file_size_from_row&gt;</span></span></em>, <em class="sig-param"><span class="n"><span class="pre">'guid':</span> <span class="pre">&lt;function</span> <span class="pre">_get_guid_from_row&gt;</span></span></em>, <em class="sig-param"><span class="n"><span class="pre">'md5':</span> <span class="pre">&lt;function</span> <span class="pre">_get_md5_from_row&gt;</span></span></em>, <em class="sig-param"><span class="n"><span class="pre">'urls':</span> <span class="pre">&lt;function</span> <span class="pre">_get_urls_from_row&gt;}</span></span></em>, <em class="sig-param"><span class="n"><span class="pre">manifest_file_delimiter=None</span></span></em>, <em class="sig-param"><span class="n"><span class="pre">output_filename='verify-manifest-errors-1696885653.7007155.log'</span></span></em><span class="sig-paren">)</span><a class="reference internal" href="../_modules/gen3/tools/indexing/verify_manifest.html#async_verify_object_manifest"><span class="viewcode-link"><span class="pre">[source]</span></span></a><a class="headerlink" href="#gen3.tools.indexing.verify_manifest.async_verify_object_manifest" title="Link to this definition"></a></dt>
<em class="property"><span class="k"><span class="pre">async</span></span><span class="w"> </span></em><span class="sig-prename descclassname"><span class="pre">gen3.tools.indexing.verify_manifest.</span></span><span class="sig-name descname"><span class="pre">async_verify_object_manifest</span></span><span class="sig-paren">(</span><em class="sig-param"><span class="n"><span class="pre">commons_url</span></span></em>, <em class="sig-param"><span class="n"><span class="pre">manifest_file</span></span></em>, <em class="sig-param"><span class="n"><span class="pre">max_concurrent_requests=24</span></span></em>, <em class="sig-param"><span class="n"><span class="pre">manifest_row_parsers={'acl':</span> <span class="pre">&lt;function</span> <span class="pre">_get_acl_from_row&gt;</span></span></em>, <em class="sig-param"><span class="n"><span class="pre">'authz':</span> <span class="pre">&lt;function</span> <span class="pre">_get_authz_from_row&gt;</span></span></em>, <em class="sig-param"><span class="n"><span class="pre">'file_name':</span> <span class="pre">&lt;function</span> <span class="pre">_get_file_name_from_row&gt;</span></span></em>, <em class="sig-param"><span class="n"><span class="pre">'file_size':</span> <span class="pre">&lt;function</span> <span class="pre">_get_file_size_from_row&gt;</span></span></em>, <em class="sig-param"><span class="n"><span class="pre">'guid':</span> <span class="pre">&lt;function</span> <span class="pre">_get_guid_from_row&gt;</span></span></em>, <em class="sig-param"><span class="n"><span class="pre">'md5':</span> <span class="pre">&lt;function</span> <span class="pre">_get_md5_from_row&gt;</span></span></em>, <em class="sig-param"><span class="n"><span class="pre">'urls':</span> <span class="pre">&lt;function</span> <span class="pre">_get_urls_from_row&gt;}</span></span></em>, <em class="sig-param"><span class="n"><span class="pre">manifest_file_delimiter=None</span></span></em>, <em class="sig-param"><span class="n"><span class="pre">output_filename='verify-manifest-errors-1697467909.0874708.log'</span></span></em><span class="sig-paren">)</span><a class="reference internal" href="../_modules/gen3/tools/indexing/verify_manifest.html#async_verify_object_manifest"><span class="viewcode-link"><span class="pre">[source]</span></span></a><a class="headerlink" href="#gen3.tools.indexing.verify_manifest.async_verify_object_manifest" title="Link to this definition"></a></dt>
<dd><p>Verify all file object records into a manifest csv</p>
<dl class="field-list simple">
<dt class="field-odd">Parameters<span class="colon">:</span></dt>
Expand Down
2 changes: 1 addition & 1 deletion docs/_build/html/tools/metadata.html
Original file line number Diff line number Diff line change
Expand Up @@ -101,7 +101,7 @@ <h1>Metadata Tools<a class="headerlink" href="#metadata-tools" title="Link to th

<dl class="py function">
<dt class="sig sig-object py" id="gen3.tools.metadata.ingest_manifest.async_ingest_metadata_manifest">
<em class="property"><span class="k"><span class="pre">async</span></span><span class="w"> </span></em><span class="sig-prename descclassname"><span class="pre">gen3.tools.metadata.ingest_manifest.</span></span><span class="sig-name descname"><span class="pre">async_ingest_metadata_manifest</span></span><span class="sig-paren">(</span><em class="sig-param"><span class="n"><span class="pre">commons_url</span></span></em>, <em class="sig-param"><span class="n"><span class="pre">manifest_file</span></span></em>, <em class="sig-param"><span class="n"><span class="pre">metadata_source</span></span></em>, <em class="sig-param"><span class="n"><span class="pre">auth=None</span></span></em>, <em class="sig-param"><span class="n"><span class="pre">max_concurrent_requests=24</span></span></em>, <em class="sig-param"><span class="n"><span class="pre">manifest_row_parsers={'guid_for_row':</span> <span class="pre">&lt;function</span> <span class="pre">_get_guid_for_row&gt;</span></span></em>, <em class="sig-param"><span class="n"><span class="pre">'indexed_file_object_guid':</span> <span class="pre">&lt;function</span> <span class="pre">_query_for_associated_indexd_record_guid&gt;}</span></span></em>, <em class="sig-param"><span class="n"><span class="pre">manifest_file_delimiter=None</span></span></em>, <em class="sig-param"><span class="n"><span class="pre">output_filename='ingest-metadata-manifest-errors-1696885654.1520922.log'</span></span></em>, <em class="sig-param"><span class="n"><span class="pre">get_guid_from_file=True</span></span></em>, <em class="sig-param"><span class="n"><span class="pre">metadata_type=None</span></span></em><span class="sig-paren">)</span><a class="reference internal" href="../_modules/gen3/tools/metadata/ingest_manifest.html#async_ingest_metadata_manifest"><span class="viewcode-link"><span class="pre">[source]</span></span></a><a class="headerlink" href="#gen3.tools.metadata.ingest_manifest.async_ingest_metadata_manifest" title="Link to this definition"></a></dt>
<em class="property"><span class="k"><span class="pre">async</span></span><span class="w"> </span></em><span class="sig-prename descclassname"><span class="pre">gen3.tools.metadata.ingest_manifest.</span></span><span class="sig-name descname"><span class="pre">async_ingest_metadata_manifest</span></span><span class="sig-paren">(</span><em class="sig-param"><span class="n"><span class="pre">commons_url</span></span></em>, <em class="sig-param"><span class="n"><span class="pre">manifest_file</span></span></em>, <em class="sig-param"><span class="n"><span class="pre">metadata_source</span></span></em>, <em class="sig-param"><span class="n"><span class="pre">auth=None</span></span></em>, <em class="sig-param"><span class="n"><span class="pre">max_concurrent_requests=24</span></span></em>, <em class="sig-param"><span class="n"><span class="pre">manifest_row_parsers={'guid_for_row':</span> <span class="pre">&lt;function</span> <span class="pre">_get_guid_for_row&gt;</span></span></em>, <em class="sig-param"><span class="n"><span class="pre">'indexed_file_object_guid':</span> <span class="pre">&lt;function</span> <span class="pre">_query_for_associated_indexd_record_guid&gt;}</span></span></em>, <em class="sig-param"><span class="n"><span class="pre">manifest_file_delimiter=None</span></span></em>, <em class="sig-param"><span class="n"><span class="pre">output_filename='ingest-metadata-manifest-errors-1697467909.51657.log'</span></span></em>, <em class="sig-param"><span class="n"><span class="pre">get_guid_from_file=True</span></span></em>, <em class="sig-param"><span class="n"><span class="pre">metadata_type=None</span></span></em><span class="sig-paren">)</span><a class="reference internal" href="../_modules/gen3/tools/metadata/ingest_manifest.html#async_ingest_metadata_manifest"><span class="viewcode-link"><span class="pre">[source]</span></span></a><a class="headerlink" href="#gen3.tools.metadata.ingest_manifest.async_ingest_metadata_manifest" title="Link to this definition"></a></dt>
<dd><p>Ingest all metadata records into a manifest csv</p>
<dl class="field-list simple">
<dt class="field-odd">Parameters<span class="colon">:</span></dt>
Expand Down

0 comments on commit 0e0bf46

Please sign in to comment.