From 5848967d732a668b48e4527e9b08a5652529a24a Mon Sep 17 00:00:00 2001 From: Calvin Condon Date: Mon, 24 Jun 2024 15:07:00 -0400 Subject: [PATCH 01/25] fixed broken link --- sphinx-doc/_templates/page.html | 2 +- 1 file changed, 1 insertion(+), 1 deletion(-) diff --git a/sphinx-doc/_templates/page.html b/sphinx-doc/_templates/page.html index eb096c38ec..ec236453a9 100644 --- a/sphinx-doc/_templates/page.html +++ b/sphinx-doc/_templates/page.html @@ -30,7 +30,7 @@
-

Development of {{ project }} is led by the Glotzer Group at the University of Michigan (supported by NSF DMR 1808342) with many external contributions. +

Development of {{ project }} is led by the Glotzer Group at the University of Michigan (supported by NSF DMR 1808342) with many external contributions.

{%- if show_copyright %} From c2ca941409a8840d0736a92c3a3e955d7f9e64f5 Mon Sep 17 00:00:00 2001 From: Calvin Condon Date: Thu, 27 Jun 2024 14:46:14 -0400 Subject: [PATCH 02/25] added link checker to test.yaml --- .github/workflows/test.yaml | 21 +++++++++++++++++++++ 1 file changed, 21 insertions(+) diff --git a/.github/workflows/test.yaml b/.github/workflows/test.yaml index 3f809d189f..c801fc5321 100644 --- a/.github/workflows/test.yaml +++ b/.github/workflows/test.yaml @@ -107,6 +107,27 @@ jobs: test_runner: [self-hosted,GPU] test_docker_options: '--gpus=all --device /dev/nvidia0 --device /dev/nvidia1 --device /dev/nvidia-uvm --device /dev/nvidia-uvm-tools --device /dev/nvidiactl' + build: + runs-on: ubuntu-latest + steps: + - name: Check out repo + uses: actions/checkout@a5ac7e51b41094c92402da3b24376905380afc29 # v4.1.6 + with: + submodules: true + - name: Set up Python + uses: actions/setup-python@82c7e631bb3cdc910f68e0081d67478d79c6982d # v5.1.0 + with: + python-version: "3.12" + - name: Setup uv + uses: glotzerlab/workflows/setup-uv@5cfac9da9cb78e16ae97a9119b6fd13c1c2d6f5e # 0.1.0 + - name: Install dependencies + run: uv pip install -r sphinx-doc/requirements.txt + - name: Build Sphinx Docs + run: sphinx-build -b html sphinx-doc doc_build + - name: Link Checker + id: lychee + uses: lycheeverse/lychee-action@v1 + tests_complete: name: Unit test if: always() From b3a7d5ba2c291095696235ab68b55a14d2a51349 Mon Sep 17 00:00:00 2001 From: Calvin Condon <145710053+chcondon@users.noreply.github.com> Date: Thu, 18 Jul 2024 13:23:05 -0400 Subject: [PATCH 03/25] Update .github/workflows/test.yaml Co-authored-by: Joshua A. Anderson --- .github/workflows/test.yaml | 2 +- 1 file changed, 1 insertion(+), 1 deletion(-) diff --git a/.github/workflows/test.yaml b/.github/workflows/test.yaml index c801fc5321..6cbfe02a7f 100644 --- a/.github/workflows/test.yaml +++ b/.github/workflows/test.yaml @@ -121,7 +121,7 @@ jobs: - name: Setup uv uses: glotzerlab/workflows/setup-uv@5cfac9da9cb78e16ae97a9119b6fd13c1c2d6f5e # 0.1.0 - name: Install dependencies - run: uv pip install -r sphinx-doc/requirements.txt + run: uv pip install -r sphinx-doc/requirements.txt --system - name: Build Sphinx Docs run: sphinx-build -b html sphinx-doc doc_build - name: Link Checker From 3bc5cb11a8601c449f042b638a1744186b64eda2 Mon Sep 17 00:00:00 2001 From: "pre-commit-ci[bot]" <66853113+pre-commit-ci[bot]@users.noreply.github.com> Date: Thu, 18 Jul 2024 17:34:42 +0000 Subject: [PATCH 04/25] [pre-commit.ci] auto fixes from pre-commit.com hooks for more information, see https://pre-commit.ci --- .github/workflows/test.yaml | 2 +- 1 file changed, 1 insertion(+), 1 deletion(-) diff --git a/.github/workflows/test.yaml b/.github/workflows/test.yaml index 6cbfe02a7f..0657a2e3fa 100644 --- a/.github/workflows/test.yaml +++ b/.github/workflows/test.yaml @@ -127,7 +127,7 @@ jobs: - name: Link Checker id: lychee uses: lycheeverse/lychee-action@v1 - + tests_complete: name: Unit test if: always() From a2e7b4725be6ca0beb99e6a394d9c963957b9eed Mon Sep 17 00:00:00 2001 From: Calvin Condon <145710053+chcondon@users.noreply.github.com> Date: Thu, 18 Jul 2024 13:38:40 -0400 Subject: [PATCH 05/25] Troubleshooting PandocMissing error --- .github/workflows/test.yaml | 2 ++ 1 file changed, 2 insertions(+) diff --git a/.github/workflows/test.yaml b/.github/workflows/test.yaml index 0657a2e3fa..ff5ba644d6 100644 --- a/.github/workflows/test.yaml +++ b/.github/workflows/test.yaml @@ -122,6 +122,8 @@ jobs: uses: glotzerlab/workflows/setup-uv@5cfac9da9cb78e16ae97a9119b6fd13c1c2d6f5e # 0.1.0 - name: Install dependencies run: uv pip install -r sphinx-doc/requirements.txt --system + - name: Verify pandoc installation + run: pandoc --version - name: Build Sphinx Docs run: sphinx-build -b html sphinx-doc doc_build - name: Link Checker From bf194c5d936873a51f7a5be8f5f2c98e2f8c8734 Mon Sep 17 00:00:00 2001 From: Calvin Condon <145710053+chcondon@users.noreply.github.com> Date: Thu, 18 Jul 2024 13:45:49 -0400 Subject: [PATCH 06/25] Troubleshooting didn't work --- .github/workflows/test.yaml | 2 -- 1 file changed, 2 deletions(-) diff --git a/.github/workflows/test.yaml b/.github/workflows/test.yaml index ff5ba644d6..0657a2e3fa 100644 --- a/.github/workflows/test.yaml +++ b/.github/workflows/test.yaml @@ -122,8 +122,6 @@ jobs: uses: glotzerlab/workflows/setup-uv@5cfac9da9cb78e16ae97a9119b6fd13c1c2d6f5e # 0.1.0 - name: Install dependencies run: uv pip install -r sphinx-doc/requirements.txt --system - - name: Verify pandoc installation - run: pandoc --version - name: Build Sphinx Docs run: sphinx-build -b html sphinx-doc doc_build - name: Link Checker From 6f682a62a2a68755512101ebccc60585d62d5743 Mon Sep 17 00:00:00 2001 From: Calvin Condon <145710053+chcondon@users.noreply.github.com> Date: Thu, 18 Jul 2024 14:48:54 -0400 Subject: [PATCH 07/25] Install pandoc --- .github/workflows/test.yaml | 2 ++ 1 file changed, 2 insertions(+) diff --git a/.github/workflows/test.yaml b/.github/workflows/test.yaml index 0657a2e3fa..dcbf9da7ff 100644 --- a/.github/workflows/test.yaml +++ b/.github/workflows/test.yaml @@ -122,6 +122,8 @@ jobs: uses: glotzerlab/workflows/setup-uv@5cfac9da9cb78e16ae97a9119b6fd13c1c2d6f5e # 0.1.0 - name: Install dependencies run: uv pip install -r sphinx-doc/requirements.txt --system + - name: Install tools + run: sudo apt-get install pandoc - name: Build Sphinx Docs run: sphinx-build -b html sphinx-doc doc_build - name: Link Checker From 5a56330ca095caa4955970c99f32e6e130d40600 Mon Sep 17 00:00:00 2001 From: Calvin Condon Date: Thu, 1 Aug 2024 12:30:42 -0400 Subject: [PATCH 08/25] fail when there are broken links, exclude external files --- .github/workflows/test.yaml | 3 +++ 1 file changed, 3 insertions(+) diff --git a/.github/workflows/test.yaml b/.github/workflows/test.yaml index dcbf9da7ff..a425f4bf3b 100644 --- a/.github/workflows/test.yaml +++ b/.github/workflows/test.yaml @@ -135,6 +135,9 @@ jobs: if: always() needs: [typical] runs-on: ubuntu-latest + with: + args: --no-progress --exclude-path hoomd/extern + fail: true steps: - run: jq --exit-status 'all(.result == "success")' <<< '${{ toJson(needs) }}' From 9841ba198964f7330ed9df68ad30dc3dbaefb6f1 Mon Sep 17 00:00:00 2001 From: Calvin Condon Date: Thu, 1 Aug 2024 12:37:38 -0400 Subject: [PATCH 09/25] stuff was deleted --- .github/workflows/test.yaml | 3 +++ 1 file changed, 3 insertions(+) diff --git a/.github/workflows/test.yaml b/.github/workflows/test.yaml index 4af03c565a..4f919a9188 100644 --- a/.github/workflows/test.yaml +++ b/.github/workflows/test.yaml @@ -117,6 +117,9 @@ jobs: - name: Link Checker id: lychee uses: lycheeverse/lychee-action@v1 + with: + args: -n --exclude-path hoomd/extern + fail: true tests_complete: name: Unit test From fe0990a1af5304d68948289653bfd198460fe75b Mon Sep 17 00:00:00 2001 From: Calvin Condon Date: Thu, 1 Aug 2024 12:44:57 -0400 Subject: [PATCH 10/25] fixing excluded files --- .github/workflows/test.yaml | 2 +- 1 file changed, 1 insertion(+), 1 deletion(-) diff --git a/.github/workflows/test.yaml b/.github/workflows/test.yaml index 4f919a9188..6860e01d7b 100644 --- a/.github/workflows/test.yaml +++ b/.github/workflows/test.yaml @@ -118,7 +118,7 @@ jobs: id: lychee uses: lycheeverse/lychee-action@v1 with: - args: -n --exclude-path hoomd/extern + args: -n --exclude-path hoomd/extern -- fail: true tests_complete: From 2a1164db1eedbb338e41144ee0830b20c43647bb Mon Sep 17 00:00:00 2001 From: Calvin Condon Date: Thu, 1 Aug 2024 12:52:04 -0400 Subject: [PATCH 11/25] adding file types --- .github/workflows/test.yaml | 2 +- 1 file changed, 1 insertion(+), 1 deletion(-) diff --git a/.github/workflows/test.yaml b/.github/workflows/test.yaml index 6860e01d7b..15425b6fd2 100644 --- a/.github/workflows/test.yaml +++ b/.github/workflows/test.yaml @@ -118,7 +118,7 @@ jobs: id: lychee uses: lycheeverse/lychee-action@v1 with: - args: -n --exclude-path hoomd/extern -- + args: -n --exclude-path hoomd/extern -- './**/*.md' './**/*.html' './**/*.rst' fail: true tests_complete: From 755c7db0f6f41af0db3f4227b5a5762a9d4fc723 Mon Sep 17 00:00:00 2001 From: Calvin Condon Date: Thu, 1 Aug 2024 14:40:54 -0400 Subject: [PATCH 12/25] geting rid of 500 error --- .github/workflows/test.yaml | 4 +++- 1 file changed, 3 insertions(+), 1 deletion(-) diff --git a/.github/workflows/test.yaml b/.github/workflows/test.yaml index 15425b6fd2..e85ca31403 100644 --- a/.github/workflows/test.yaml +++ b/.github/workflows/test.yaml @@ -118,8 +118,10 @@ jobs: id: lychee uses: lycheeverse/lychee-action@v1 with: - args: -n --exclude-path hoomd/extern -- './**/*.md' './**/*.html' './**/*.rst' + args: -n --exclude-path hoomd/extern --exclude https://glotzerlab.engin.umich.edu -- './**/*.md' './**/*.html' './**/*.rst' fail: true + format: json + tests_complete: name: Unit test From 8efefcddcfd673b10b2378321e511342a358ed95 Mon Sep 17 00:00:00 2001 From: Calvin Condon Date: Thu, 1 Aug 2024 19:04:54 -0400 Subject: [PATCH 13/25] fixed some broken links, excluded doi and gitlab --- .github/workflows/test.yaml | 3 +-- ARCHITECTURE.md | 2 +- README.md | 2 +- sphinx-doc/license.rst | 4 ++-- sphinx-doc/migrating.rst | 4 ++-- 5 files changed, 7 insertions(+), 8 deletions(-) diff --git a/.github/workflows/test.yaml b/.github/workflows/test.yaml index e85ca31403..b26899ee2f 100644 --- a/.github/workflows/test.yaml +++ b/.github/workflows/test.yaml @@ -118,9 +118,8 @@ jobs: id: lychee uses: lycheeverse/lychee-action@v1 with: - args: -n --exclude-path hoomd/extern --exclude https://glotzerlab.engin.umich.edu -- './**/*.md' './**/*.html' './**/*.rst' + args: -n --exclude-path hoomd/extern --exclude https://glotzerlab.engin.umich.edu doi.org gitlab.com -- './**/*.md' './**/*.html' './**/*.rst' fail: true - format: json tests_complete: diff --git a/ARCHITECTURE.md b/ARCHITECTURE.md index 5b2306ea11..45400f43bb 100644 --- a/ARCHITECTURE.md +++ b/ARCHITECTURE.md @@ -398,7 +398,7 @@ classes is automated through previously described classes. HOOMD-blue version 3 allows for much more interaction with Python objects within its C++ core. One feature is custom actions (see the tutorial -https://hoomd-blue.readthedocs.io/en/latest/tutorial/03-Custom-Actions-In-Python/00-index.html +https://hoomd-blue.readthedocs.io/en/latest/tutorial/04-Custom-Actions-In-Python/00-index.html or API documentation for more introductory information). When using custom actions internally for HOOMD, the classes `hoomd.custom._InternalAction` and one of the `hoomd.custom._InternalOperation` subclasses are to be used. They allow diff --git a/README.md b/README.md index cc3dcde8ee..a04fd495dc 100644 --- a/README.md +++ b/README.md @@ -3,7 +3,7 @@ [![Citing HOOMD](https://img.shields.io/badge/cite-hoomd-blue.svg)](https://hoomd-blue.readthedocs.io/en/latest/citing.html) [![conda-forge](https://img.shields.io/conda/vn/conda-forge/hoomd.svg?style=flat)](https://anaconda.org/conda-forge/hoomd) [![conda-forge Downloads](https://img.shields.io/conda/dn/conda-forge/hoomd.svg?style=flat)](https://anaconda.org/conda-forge/hoomd) -[![GitHub Actions](https://github.com/glotzerlab/hoomd-blue/actions/workflows/test.yml/badge.svg?branch=trunk-patch)](https://github.com/glotzerlab/hoomd-blue/actions/workflows/test.yml) +[![GitHub Actions](https://github.com/glotzerlab/hoomd-blue/actions/workflows//test.yml/badge.svg?branch=trunk-patch)](https://github.com/glotzerlab/hoomd-blue/actions/workflows/test.yml) [![Read the Docs](https://img.shields.io/readthedocs/hoomd-blue/latest.svg)](https://hoomd-blue.readthedocs.io/en/latest/?badge=latest) [![Contributors](https://img.shields.io/github/contributors-anon/glotzerlab/hoomd-blue.svg?style=flat)](https://hoomd-blue.readthedocs.io/en/latest/credits.html) [![License](https://img.shields.io/badge/license-BSD--3--Clause-green.svg)](LICENSE) diff --git a/sphinx-doc/license.rst b/sphinx-doc/license.rst index 933e86db58..076fd0630c 100644 --- a/sphinx-doc/license.rst +++ b/sphinx-doc/license.rst @@ -9,7 +9,7 @@ License Libraries --------- -**HOOMD:** HOOMD-blue is a continuation of the HOOMD project (http://www.ameslab.gov/hoomd/). The code from the original project is used under the following license:: +**HOOMD:** HOOMD-blue is a continuation of the HOOMD project (https://www.ameslab.gov/work-us/open-source-software). The code from the original project is used under the following license:: Highly Optimized Object-Oriented Molecular Dynamics (HOOMD) Open Source Software License @@ -122,7 +122,7 @@ following license:: (INCLUDING NEGLIGENCE OR OTHERWISE) ARISING IN ANY WAY OUT OF THE USE OF THIS SOFTWARE, EVEN IF ADVISED OF THE POSSIBILITY OF SUCH DAMAGE. -`CUB `_, used under the following license:: +`CUB `_, used under the following license:: Copyright (c) 2011, Duane Merrill. All rights reserved. Copyright (c) 2011-2016, NVIDIA CORPORATION. All rights reserved. diff --git a/sphinx-doc/migrating.rst b/sphinx-doc/migrating.rst index 9dbcf30638..375a07cff3 100644 --- a/sphinx-doc/migrating.rst +++ b/sphinx-doc/migrating.rst @@ -292,9 +292,9 @@ HOOMD v3 removes old APIs, unused functionality, and features better served by o * - ``deprecated.init.read_xml`` - `Simulation.create_state_from_gsd` * - ``deprecated.init.create_random`` - - `mBuild `_, `packmol `_, or user script. + - `mBuild `_, `packmol `_, or user script. * - ``deprecated.init.create_random_polymers`` - - `mBuild `_, `packmol `_, or user script. + - `mBuild `_, `packmol `_, or user script. :py:mod:`hoomd.hpmc`: From 584fa5f7c646dcbac8700237975ad5eae570ba1a Mon Sep 17 00:00:00 2001 From: Calvin Condon Date: Thu, 1 Aug 2024 19:09:38 -0400 Subject: [PATCH 14/25] fixes --- .github/workflows/test.yaml | 2 +- 1 file changed, 1 insertion(+), 1 deletion(-) diff --git a/.github/workflows/test.yaml b/.github/workflows/test.yaml index b26899ee2f..a32dfe7606 100644 --- a/.github/workflows/test.yaml +++ b/.github/workflows/test.yaml @@ -118,7 +118,7 @@ jobs: id: lychee uses: lycheeverse/lychee-action@v1 with: - args: -n --exclude-path hoomd/extern --exclude https://glotzerlab.engin.umich.edu doi.org gitlab.com -- './**/*.md' './**/*.html' './**/*.rst' + args: -n --exclude-path hoomd/extern --exclude https://glotzerlab.engin.umich.edu --exclude doi.org --exclude gitlab.com -- './**/*.md' './**/*.html' './**/*.rst' fail: true From fc23e0a2828969738f4e17c63125391af27bb305 Mon Sep 17 00:00:00 2001 From: Calvin Condon Date: Thu, 1 Aug 2024 19:27:50 -0400 Subject: [PATCH 15/25] ideally, final commit --- .github/workflows/test.yaml | 6 +++++- 1 file changed, 5 insertions(+), 1 deletion(-) diff --git a/.github/workflows/test.yaml b/.github/workflows/test.yaml index a32dfe7606..e98532eaff 100644 --- a/.github/workflows/test.yaml +++ b/.github/workflows/test.yaml @@ -118,7 +118,11 @@ jobs: id: lychee uses: lycheeverse/lychee-action@v1 with: - args: -n --exclude-path hoomd/extern --exclude https://glotzerlab.engin.umich.edu --exclude doi.org --exclude gitlab.com -- './**/*.md' './**/*.html' './**/*.rst' + args: -n --exclude-path hoomd/extern sphinx-doc/_templates/page.html file:///home/runner/work/hoomd-blue/hoomd-blue + --exclude https://glotzerlab.engin.umich.edu + --exclude doi.org + --exclude gitlab.com -- + './**/*.md' './**/*.html' './**/*.rst' fail: true From ecacf49256f933bfb52bf27f8cb113a48bc57cdb Mon Sep 17 00:00:00 2001 From: Calvin Condon Date: Tue, 6 Aug 2024 18:11:13 -0400 Subject: [PATCH 16/25] testing --- .github/workflows/test.yaml | 2 +- 1 file changed, 1 insertion(+), 1 deletion(-) diff --git a/.github/workflows/test.yaml b/.github/workflows/test.yaml index e98532eaff..dc4821008c 100644 --- a/.github/workflows/test.yaml +++ b/.github/workflows/test.yaml @@ -118,7 +118,7 @@ jobs: id: lychee uses: lycheeverse/lychee-action@v1 with: - args: -n --exclude-path hoomd/extern sphinx-doc/_templates/page.html file:///home/runner/work/hoomd-blue/hoomd-blue + args: -n --exclude-path hoomd/extern sphinx-doc/_templates/page.html doc_build/module --exclude https://glotzerlab.engin.umich.edu --exclude doi.org --exclude gitlab.com -- From 449ea72030c8d1eab5794f0626b75db5d6764810 Mon Sep 17 00:00:00 2001 From: Calvin Condon Date: Tue, 6 Aug 2024 18:18:53 -0400 Subject: [PATCH 17/25] ignore module files --- .github/workflows/test.yaml | 4 ++-- 1 file changed, 2 insertions(+), 2 deletions(-) diff --git a/.github/workflows/test.yaml b/.github/workflows/test.yaml index dc4821008c..505cb2ee30 100644 --- a/.github/workflows/test.yaml +++ b/.github/workflows/test.yaml @@ -118,10 +118,10 @@ jobs: id: lychee uses: lycheeverse/lychee-action@v1 with: - args: -n --exclude-path hoomd/extern sphinx-doc/_templates/page.html doc_build/module + args: -n --exclude-path hoomd/extern sphinx-doc/_templates/page.html doc_build/*module*.html --exclude https://glotzerlab.engin.umich.edu --exclude doi.org - --exclude gitlab.com -- + --exclude gitlab.com './**/*.md' './**/*.html' './**/*.rst' fail: true From eff7c22675ddeffba3ac84ad2d4adf74819fa8b9 Mon Sep 17 00:00:00 2001 From: Calvin Condon Date: Tue, 6 Aug 2024 18:29:27 -0400 Subject: [PATCH 18/25] reformatted exlcude-path --- .github/workflows/test.yaml | 5 ++++- 1 file changed, 4 insertions(+), 1 deletion(-) diff --git a/.github/workflows/test.yaml b/.github/workflows/test.yaml index 505cb2ee30..0ba2a3b378 100644 --- a/.github/workflows/test.yaml +++ b/.github/workflows/test.yaml @@ -118,7 +118,10 @@ jobs: id: lychee uses: lycheeverse/lychee-action@v1 with: - args: -n --exclude-path hoomd/extern sphinx-doc/_templates/page.html doc_build/*module*.html + args: -n --exclude-path hoomd/extern + --exclude-path sphinx-doc/_templates/page.html + --exclude-path doc_build/module*.html + --exclude-path ARCHITECTURE.md --exclude https://glotzerlab.engin.umich.edu --exclude doi.org --exclude gitlab.com From 6bdaf80f10004b4e26e758d098663e728c9de26f Mon Sep 17 00:00:00 2001 From: Calvin Condon Date: Tue, 6 Aug 2024 18:35:25 -0400 Subject: [PATCH 19/25] added quotes --- .github/workflows/test.yaml | 8 ++++---- 1 file changed, 4 insertions(+), 4 deletions(-) diff --git a/.github/workflows/test.yaml b/.github/workflows/test.yaml index 0ba2a3b378..bb669db13c 100644 --- a/.github/workflows/test.yaml +++ b/.github/workflows/test.yaml @@ -118,10 +118,10 @@ jobs: id: lychee uses: lycheeverse/lychee-action@v1 with: - args: -n --exclude-path hoomd/extern - --exclude-path sphinx-doc/_templates/page.html - --exclude-path doc_build/module*.html - --exclude-path ARCHITECTURE.md + args: -n --exclude-path 'hoomd/extern' + --exclude-path 'sphinx-doc/_templates/page.html' + --exclude-path 'doc_build/*module*.html' + --exclude-path 'ARCHITECTURE.md' --exclude https://glotzerlab.engin.umich.edu --exclude doi.org --exclude gitlab.com From 0bf3c59e3836725a0c686373298374913bb08e09 Mon Sep 17 00:00:00 2001 From: Calvin Condon Date: Tue, 6 Aug 2024 18:47:58 -0400 Subject: [PATCH 20/25] troubleshooting --- .github/workflows/test.yaml | 3 ++- 1 file changed, 2 insertions(+), 1 deletion(-) diff --git a/.github/workflows/test.yaml b/.github/workflows/test.yaml index bb669db13c..b83eb5ba54 100644 --- a/.github/workflows/test.yaml +++ b/.github/workflows/test.yaml @@ -118,8 +118,9 @@ jobs: id: lychee uses: lycheeverse/lychee-action@v1 with: - args: -n --exclude-path 'hoomd/extern' + args: -n --exclude-path 'sphinx-doc/_templates/page.html' + --exclude-path 'hoomd/extern' --exclude-path 'doc_build/*module*.html' --exclude-path 'ARCHITECTURE.md' --exclude https://glotzerlab.engin.umich.edu From e99edc3ceb27b93c5e7b52ff8e3326e387662d70 Mon Sep 17 00:00:00 2001 From: "Joshua A. Anderson" Date: Thu, 22 Aug 2024 12:26:23 -0400 Subject: [PATCH 21/25] Revise link checker settings. --- .github/workflows/test.yaml | 13 ++++++------- ARCHITECTURE.md | 8 ++------ README.md | 2 +- hoomd/md/bond.py | 2 +- sphinx-doc/style.rst | 2 +- 5 files changed, 11 insertions(+), 16 deletions(-) diff --git a/.github/workflows/test.yaml b/.github/workflows/test.yaml index b83eb5ba54..ce1c88fedd 100644 --- a/.github/workflows/test.yaml +++ b/.github/workflows/test.yaml @@ -95,7 +95,8 @@ jobs: - config: [gcc, 11, -py, 310, -mpi, -tbb] - config: [gcc, 10, -py, 310, -mpi, -tbb] - build: + check-links: + name: "Check links" runs-on: ubuntu-latest steps: - name: Check out repo @@ -116,18 +117,16 @@ jobs: run: sphinx-build -b html sphinx-doc doc_build - name: Link Checker id: lychee - uses: lycheeverse/lychee-action@v1 + uses: lycheeverse/lychee-action@2b973e86fc7b1f6b36a93795fe2c9c6ae1118621 # v1.10.0 with: args: -n --exclude-path 'sphinx-doc/_templates/page.html' - --exclude-path 'hoomd/extern' - --exclude-path 'doc_build/*module*.html' - --exclude-path 'ARCHITECTURE.md' - --exclude https://glotzerlab.engin.umich.edu + --exclude-path 'hoomd/extern' --exclude doi.org - --exclude gitlab.com './**/*.md' './**/*.html' './**/*.rst' fail: true + # --exclude-path 'doc_build/*module*.html' + # --exclude https://glotzerlab.engin.umich.edu tests_complete: diff --git a/ARCHITECTURE.md b/ARCHITECTURE.md index 45400f43bb..d226b78250 100644 --- a/ARCHITECTURE.md +++ b/ARCHITECTURE.md @@ -19,19 +19,15 @@ Each minor and major release of HOOMD-blue at a minimum supports: ### Continuous integration [Github Actions] performs continuous integration testing on HOOMD-blue. GitHub -Actions compiles HOOMD-blue, runs the unit tests, and and reports the +Actions compiles HOOMD-blue, runs the unit tests, and reports the status to GitHub pull requests. A number of parallel builds test a variety of compiler and build configurations as defined above. Visit the [workflows] page to find recent builds. The pipeline configuration -files are in [.github/workflows/] and are built from Jinja templates in -[.github/workflows/templates/] using `make_workflows.py` which is automatically -run by `pre-commit`. To make changes to the workflows, edit the templates. +files are in `.github/workflows/`. [GitHub Actions]: https://docs.github.com/en/actions [workflows]: https://github.com/glotzerlab/hoomd-blue/actions -[.github/workflows/]: .github/workflows/ -[.github/workflows/templates/]: .github/workflows/templates/ ## Build system diff --git a/README.md b/README.md index a04fd495dc..6f4c76a3af 100644 --- a/README.md +++ b/README.md @@ -3,7 +3,7 @@ [![Citing HOOMD](https://img.shields.io/badge/cite-hoomd-blue.svg)](https://hoomd-blue.readthedocs.io/en/latest/citing.html) [![conda-forge](https://img.shields.io/conda/vn/conda-forge/hoomd.svg?style=flat)](https://anaconda.org/conda-forge/hoomd) [![conda-forge Downloads](https://img.shields.io/conda/dn/conda-forge/hoomd.svg?style=flat)](https://anaconda.org/conda-forge/hoomd) -[![GitHub Actions](https://github.com/glotzerlab/hoomd-blue/actions/workflows//test.yml/badge.svg?branch=trunk-patch)](https://github.com/glotzerlab/hoomd-blue/actions/workflows/test.yml) +[![GitHub Actions](https://github.com/glotzerlab/hoomd-blue/actions/workflows//test.yaml/badge.svg?branch=trunk-patch)](https://github.com/glotzerlab/hoomd-blue/actions/workflows/test.yaml) [![Read the Docs](https://img.shields.io/readthedocs/hoomd-blue/latest.svg)](https://hoomd-blue.readthedocs.io/en/latest/?badge=latest) [![Contributors](https://img.shields.io/github/contributors-anon/glotzerlab/hoomd-blue.svg?style=flat)](https://hoomd-blue.readthedocs.io/en/latest/credits.html) [![License](https://img.shields.io/badge/license-BSD--3--Clause-green.svg)](LICENSE) diff --git a/hoomd/md/bond.py b/hoomd/md/bond.py index 6e469128e4..72af360a76 100644 --- a/hoomd/md/bond.py +++ b/hoomd/md/bond.py @@ -279,7 +279,7 @@ class Tether(Bond): The tethered network is described in Refs. `Gompper, G. & Kroll, D. M. Statistical Mechanics of Membranes and Surfaces 2nd edn (eds Nelson, D. R. et al.) 359-426 (World Scientific, 2004) - `__ and + `__ and `Noguchi, H. & Gompper, G., Phys. Rev. E 72 011901 (2005) `__. diff --git a/sphinx-doc/style.rst b/sphinx-doc/style.rst index 6893f1805f..13d1a91d6f 100644 --- a/sphinx-doc/style.rst +++ b/sphinx-doc/style.rst @@ -34,7 +34,7 @@ Tools * With these plugins: * `pep8-naming `_ - * `flake8-docstrings `_ + * `flake8-docstrings `_ * `flake8-rst-docstrings `_ * Configure flake8 in your editor to see violations on save. From 8ed511549f87ff4fed130ae703a00e951d996099 Mon Sep 17 00:00:00 2001 From: "Joshua A. Anderson" Date: Thu, 22 Aug 2024 12:35:03 -0400 Subject: [PATCH 22/25] Fix more broken links.: --- .github/workflows/test.yaml | 4 +--- hoomd/data/array.py | 2 +- sphinx-doc/index.rst | 4 ++-- 3 files changed, 4 insertions(+), 6 deletions(-) diff --git a/.github/workflows/test.yaml b/.github/workflows/test.yaml index ce1c88fedd..69b4f70902 100644 --- a/.github/workflows/test.yaml +++ b/.github/workflows/test.yaml @@ -122,12 +122,10 @@ jobs: args: -n --exclude-path 'sphinx-doc/_templates/page.html' --exclude-path 'hoomd/extern' + --exclude https://glotzerlab.engin.umich.edu --exclude doi.org './**/*.md' './**/*.html' './**/*.rst' fail: true - # --exclude-path 'doc_build/*module*.html' - # --exclude https://glotzerlab.engin.umich.edu - tests_complete: name: Unit test diff --git a/hoomd/data/array.py b/hoomd/data/array.py index c94f9c3dcd..05ac47c043 100644 --- a/hoomd/data/array.py +++ b/hoomd/data/array.py @@ -755,7 +755,7 @@ class HOOMDGPUArray(_NoGPU): Packages like Numba and PyTorch can use `HOOMDGPUArray` without CuPy installed. Any package that supports version 2 of the `__cuda_array_interface__ - `_ + `_ should support the direct use of `HOOMDGPUArray` objects. """ diff --git a/sphinx-doc/index.rst b/sphinx-doc/index.rst index 6f70bed1f6..e6d29fc61a 100644 --- a/sphinx-doc/index.rst +++ b/sphinx-doc/index.rst @@ -21,8 +21,8 @@ HOOMD-blue :target: https://anaconda.org/conda-forge/hoomd .. |conda-forge-Downloads| image:: https://img.shields.io/conda/dn/conda-forge/hoomd.svg?style=flat :target: https://anaconda.org/conda-forge/hoomd - .. |GitHub Actions| image:: https://github.com/glotzerlab/hoomd-blue/actions/workflows/test.yml/badge.svg?branch=trunk-patch - :target: https://github.com/glotzerlab/hoomd-blue/actions/workflows/test.yml + .. |GitHub Actions| image:: https://github.com/glotzerlab/hoomd-blue/actions/workflows/test.yaml/badge.svg?branch=trunk-patch + :target: https://github.com/glotzerlab/hoomd-blue/actions/workflows/test.yaml .. |Contributors| image:: https://img.shields.io/github/contributors-anon/glotzerlab/hoomd-blue.svg?style=flat :target: https://hoomd-blue.readthedocs.io/en/latest/credits.html .. |License| image:: https://img.shields.io/badge/license-BSD--3--Clause-green.svg From 1f33acd5d7d9ce168a3aae4fe2297e6058680ce0 Mon Sep 17 00:00:00 2001 From: "Joshua A. Anderson" Date: Thu, 22 Aug 2024 12:41:25 -0400 Subject: [PATCH 23/25] Fix yet more broken links. --- hoomd/data/array.py | 2 +- hoomd/md/constrain.py | 2 +- 2 files changed, 2 insertions(+), 2 deletions(-) diff --git a/hoomd/data/array.py b/hoomd/data/array.py index 05ac47c043..8b7ae4d804 100644 --- a/hoomd/data/array.py +++ b/hoomd/data/array.py @@ -720,7 +720,7 @@ class HOOMDGPUArray(_NoGPU): The HOOMDGPUArray object exposes a GPU data buffer using `__cuda_array_interface__ -`_. +`_. This class provides buffer access through a context manager to prevent invalid memory accesses (`hoomd.State.gpu_local_snapshot`). To avoid errors, use arrays only within the relevant context manager. For example: diff --git a/hoomd/md/constrain.py b/hoomd/md/constrain.py index 2064465691..a6bfdc7eb1 100644 --- a/hoomd/md/constrain.py +++ b/hoomd/md/constrain.py @@ -77,7 +77,7 @@ class Distance(Constraint): Where :math:`i` and :math:`j` are the the particle tags in the ``constraint_group`` and :math:`d_{ij}` is the constraint distance as given - by the `system state `_. + by the system state. The method sets the second derivative of the Lagrange multipliers with respect to time to zero, such that both the distance constraints and their From bd9fd4761c9a8aa662cdd43d8efdc98db613af24 Mon Sep 17 00:00:00 2001 From: "Joshua A. Anderson" Date: Thu, 22 Aug 2024 12:48:02 -0400 Subject: [PATCH 24/25] Remove incorrect link. --- sphinx-doc/license.rst | 2 +- 1 file changed, 1 insertion(+), 1 deletion(-) diff --git a/sphinx-doc/license.rst b/sphinx-doc/license.rst index 076fd0630c..2f818b0c16 100644 --- a/sphinx-doc/license.rst +++ b/sphinx-doc/license.rst @@ -9,7 +9,7 @@ License Libraries --------- -**HOOMD:** HOOMD-blue is a continuation of the HOOMD project (https://www.ameslab.gov/work-us/open-source-software). The code from the original project is used under the following license:: +**HOOMD:** HOOMD-blue is a continuation of the HOOMD project. The code from the original project is used under the following license:: Highly Optimized Object-Oriented Molecular Dynamics (HOOMD) Open Source Software License From 63cc7aa2395a8576a95a4eeab637ed55027365c6 Mon Sep 17 00:00:00 2001 From: "Joshua A. Anderson" Date: Fri, 23 Aug 2024 09:27:21 -0400 Subject: [PATCH 25/25] pre-commit. --- .github/workflows/test.yaml | 2 +- 1 file changed, 1 insertion(+), 1 deletion(-) diff --git a/.github/workflows/test.yaml b/.github/workflows/test.yaml index 69b4f70902..854925f061 100644 --- a/.github/workflows/test.yaml +++ b/.github/workflows/test.yaml @@ -123,7 +123,7 @@ jobs: --exclude-path 'sphinx-doc/_templates/page.html' --exclude-path 'hoomd/extern' --exclude https://glotzerlab.engin.umich.edu - --exclude doi.org + --exclude doi.org './**/*.md' './**/*.html' './**/*.rst' fail: true