From 49b50fc06231b847fd6cdfc4f62161468cb58d87 Mon Sep 17 00:00:00 2001 From: jonwzheng Date: Wed, 28 Feb 2024 15:07:16 -0500 Subject: [PATCH 01/15] Troubleshooting commit (to revert later): Modify Github workflow so that test and publish actions are inverted Also sets --dry-run to the git push step. This step is only to help troubleshoot the source of RMG docs build issues --- .github/workflows/docs.yml | 10 +++++----- 1 file changed, 5 insertions(+), 5 deletions(-) diff --git a/.github/workflows/docs.yml b/.github/workflows/docs.yml index e0acb22d41..379a337b8e 100644 --- a/.github/workflows/docs.yml +++ b/.github/workflows/docs.yml @@ -50,8 +50,10 @@ jobs: - name: Make documentation - for testing if: ${{ github.event_name != 'push' || github.repository != 'ReactionMechanismGenerator/RMG-Py' }} run: | + git config --global user.name "github-actions" + git config --global user.email "github-actions@github.com" cd documentation - sphinx-build -b html -d build/doctrees/ source/ build/html -w errors.log -W --keep-going + make html - name: Report documentation errors if: ${{ failure() }} run: | @@ -59,10 +61,8 @@ jobs: - name: Make documentation - to publish if: ${{ github.event_name == 'push' && github.repository == 'ReactionMechanismGenerator/RMG-Py' }} run: | - git config --global user.name "github-actions" - git config --global user.email "github-actions@github.com" cd documentation - make html + sphinx-build -b html -d build/doctrees/ source/ build/html -w errors.log -W --keep-going - name: Check documentation links continue-on-error: true run: | @@ -72,4 +72,4 @@ jobs: if: ${{ github.event_name == 'push' && github.repository == 'ReactionMechanismGenerator/RMG-Py' }} run: | touch build/html/.nojekyll - cd build/html; git add -A .; git commit -m "Automated documentation rebuild"; git push origin gh-pages + cd build/html; git add -A .; git commit -m "Automated documentation rebuild"; git push --dry-run origin gh-pages From 50380cbc100752012bde87063b30e4b51ab43960 Mon Sep 17 00:00:00 2001 From: jonwzheng Date: Wed, 28 Feb 2024 16:42:02 -0500 Subject: [PATCH 02/15] add logging messages to help figure out where website build workflow is going wrong --- .github/workflows/docs.yml | 6 ++++++ 1 file changed, 6 insertions(+) diff --git a/.github/workflows/docs.yml b/.github/workflows/docs.yml index 379a337b8e..422d829d98 100644 --- a/.github/workflows/docs.yml +++ b/.github/workflows/docs.yml @@ -52,7 +52,10 @@ jobs: run: | git config --global user.name "github-actions" git config --global user.email "github-actions@github.com" + ls -l + pwd cd documentation + ls -l make html - name: Report documentation errors if: ${{ failure() }} @@ -72,4 +75,7 @@ jobs: if: ${{ github.event_name == 'push' && github.repository == 'ReactionMechanismGenerator/RMG-Py' }} run: | touch build/html/.nojekyll + ls -l + pwd + ls -l build/html/ cd build/html; git add -A .; git commit -m "Automated documentation rebuild"; git push --dry-run origin gh-pages From 341111d87d174550beccd4c5b78a35a7591f0046 Mon Sep 17 00:00:00 2001 From: Jackson Burns <33505528+JacksonBurns@users.noreply.github.com> Date: Wed, 28 Feb 2024 20:32:36 -0500 Subject: [PATCH 03/15] DROP ME: run the publish step all the time for debugging purposes --- .github/workflows/docs.yml | 2 +- 1 file changed, 1 insertion(+), 1 deletion(-) diff --git a/.github/workflows/docs.yml b/.github/workflows/docs.yml index 422d829d98..5e964475e7 100644 --- a/.github/workflows/docs.yml +++ b/.github/workflows/docs.yml @@ -72,7 +72,7 @@ jobs: cd documentation sphinx-build -b linkcheck -d build/doctrees/ source/ build/linkcheck | grep -e broken -e redirect | grep -v -e 'redirect https://doi.org/' -e 'broken https://doi.org/.* 403 Client Error: Forbidden' - name: Publish documentation - if: ${{ github.event_name == 'push' && github.repository == 'ReactionMechanismGenerator/RMG-Py' }} + # if: ${{ github.event_name == 'push' && github.repository == 'ReactionMechanismGenerator/RMG-Py' }} run: | touch build/html/.nojekyll ls -l From 0d7125bfb6b529852aa4250e8986e957b327c337 Mon Sep 17 00:00:00 2001 From: Jackson Burns <33505528+JacksonBurns@users.noreply.github.com> Date: Wed, 28 Feb 2024 21:36:30 -0500 Subject: [PATCH 04/15] checkout complete branch history of `gh-pages` --- .github/workflows/docs.yml | 1 + 1 file changed, 1 insertion(+) diff --git a/.github/workflows/docs.yml b/.github/workflows/docs.yml index 5e964475e7..8d53006ced 100644 --- a/.github/workflows/docs.yml +++ b/.github/workflows/docs.yml @@ -46,6 +46,7 @@ jobs: - uses: actions/checkout@v2 with: ref: gh-pages + fetch-depth: 0 # checkout the complete git history so upstream is seen as out of date when attempting to push these updates path: build/html - name: Make documentation - for testing if: ${{ github.event_name != 'push' || github.repository != 'ReactionMechanismGenerator/RMG-Py' }} From cbcab7fcde0a6b9bfedd45e43e52e6e0f921eb80 Mon Sep 17 00:00:00 2001 From: Jackson Burns <33505528+JacksonBurns@users.noreply.github.com> Date: Thu, 29 Feb 2024 09:29:39 -0500 Subject: [PATCH 05/15] DROP ME: git status all over the place --- .github/workflows/docs.yml | 9 ++++++++- 1 file changed, 8 insertions(+), 1 deletion(-) diff --git a/.github/workflows/docs.yml b/.github/workflows/docs.yml index 8d53006ced..1c57ad4f90 100644 --- a/.github/workflows/docs.yml +++ b/.github/workflows/docs.yml @@ -79,4 +79,11 @@ jobs: ls -l pwd ls -l build/html/ - cd build/html; git add -A .; git commit -m "Automated documentation rebuild"; git push --dry-run origin gh-pages + git status + cd build/html + git status + git add -A . + git status + git commit -m "Automated documentation rebuild" + git status + git push --dry-run origin gh-pages From 747fb6d05c1518fa3101d754b0a33cbf923ce202 Mon Sep 17 00:00:00 2001 From: jonwzheng Date: Thu, 29 Feb 2024 11:43:44 -0500 Subject: [PATCH 06/15] DROPME: modify makefile to include very verbose logging information --- documentation/Makefile | 2 +- 1 file changed, 1 insertion(+), 1 deletion(-) diff --git a/documentation/Makefile b/documentation/Makefile index d42279f698..3254527068 100644 --- a/documentation/Makefile +++ b/documentation/Makefile @@ -51,7 +51,7 @@ clean: rm -rf build_temp html: - $(SPHINXBUILD) -b html $(ALLSPHINXOPTS) $(BUILDDIR)/html + $(SPHINXBUILD) -vvv -b html $(ALLSPHINXOPTS) $(BUILDDIR)/html @echo @echo "Build finished. The HTML pages are in $(BUILDDIR)/html." From ac55c082a6cf00ffbc06fd3a510a46f6d4fc6d41 Mon Sep 17 00:00:00 2001 From: jonwzheng Date: Thu, 29 Feb 2024 11:44:56 -0500 Subject: [PATCH 07/15] DROPME: add additional logging --- .github/workflows/docs.yml | 2 ++ 1 file changed, 2 insertions(+) diff --git a/.github/workflows/docs.yml b/.github/workflows/docs.yml index 1c57ad4f90..6a86087a5f 100644 --- a/.github/workflows/docs.yml +++ b/.github/workflows/docs.yml @@ -58,6 +58,8 @@ jobs: cd documentation ls -l make html + ls -l + ls -l build/html - name: Report documentation errors if: ${{ failure() }} run: | From c26be02a7a4c816f9e75aa460a3711a7890699e0 Mon Sep 17 00:00:00 2001 From: jonwzheng Date: Thu, 29 Feb 2024 12:22:41 -0500 Subject: [PATCH 08/15] DROPME: a bit toooo verbose --- documentation/Makefile | 2 +- 1 file changed, 1 insertion(+), 1 deletion(-) diff --git a/documentation/Makefile b/documentation/Makefile index 3254527068..9402169a68 100644 --- a/documentation/Makefile +++ b/documentation/Makefile @@ -51,7 +51,7 @@ clean: rm -rf build_temp html: - $(SPHINXBUILD) -vvv -b html $(ALLSPHINXOPTS) $(BUILDDIR)/html + $(SPHINXBUILD) -v -b html $(ALLSPHINXOPTS) $(BUILDDIR)/html @echo @echo "Build finished. The HTML pages are in $(BUILDDIR)/html." From 0c71dab8283ddeca08dbff123dea749be6b591c5 Mon Sep 17 00:00:00 2001 From: Jackson Burns <33505528+JacksonBurns@users.noreply.github.com> Date: Thu, 29 Feb 2024 14:16:55 -0500 Subject: [PATCH 09/15] do not clean before checkout of gh-pages, go back to shallow clone to potentially avoid having to do it --- .github/workflows/docs.yml | 3 ++- 1 file changed, 2 insertions(+), 1 deletion(-) diff --git a/.github/workflows/docs.yml b/.github/workflows/docs.yml index 6a86087a5f..961d82ea08 100644 --- a/.github/workflows/docs.yml +++ b/.github/workflows/docs.yml @@ -46,8 +46,9 @@ jobs: - uses: actions/checkout@v2 with: ref: gh-pages - fetch-depth: 0 # checkout the complete git history so upstream is seen as out of date when attempting to push these updates + clean: false path: build/html + # fetch-depth: 0 # checkout the complete git history so upstream is seen as out of date when attempting to push these updates - name: Make documentation - for testing if: ${{ github.event_name != 'push' || github.repository != 'ReactionMechanismGenerator/RMG-Py' }} run: | From cfb5f05108e04cc7adc3aa1b0fdab7c02b0edd4a Mon Sep 17 00:00:00 2001 From: Jackson Burns <33505528+JacksonBurns@users.noreply.github.com> Date: Thu, 29 Feb 2024 14:52:34 -0500 Subject: [PATCH 10/15] gotta fetch 'em all ('em being the `git` history) --- .github/workflows/docs.yml | 2 +- 1 file changed, 1 insertion(+), 1 deletion(-) diff --git a/.github/workflows/docs.yml b/.github/workflows/docs.yml index 961d82ea08..b9f511d997 100644 --- a/.github/workflows/docs.yml +++ b/.github/workflows/docs.yml @@ -48,7 +48,7 @@ jobs: ref: gh-pages clean: false path: build/html - # fetch-depth: 0 # checkout the complete git history so upstream is seen as out of date when attempting to push these updates + fetch-depth: 0 # checkout the complete git history so upstream is seen as out of date when attempting to push these updates - name: Make documentation - for testing if: ${{ github.event_name != 'push' || github.repository != 'ReactionMechanismGenerator/RMG-Py' }} run: | From 67f596a38092853a9dc4e22fa2cb4578d8909d36 Mon Sep 17 00:00:00 2001 From: Jackson Burns <33505528+JacksonBurns@users.noreply.github.com> Date: Thu, 29 Feb 2024 15:45:47 -0500 Subject: [PATCH 11/15] AHHHHHHHHHHHHHH --- .github/workflows/docs.yml | 19 +++++++++++++++++++ 1 file changed, 19 insertions(+) diff --git a/.github/workflows/docs.yml b/.github/workflows/docs.yml index b9f511d997..01e8da461b 100644 --- a/.github/workflows/docs.yml +++ b/.github/workflows/docs.yml @@ -78,15 +78,34 @@ jobs: - name: Publish documentation # if: ${{ github.event_name == 'push' && github.repository == 'ReactionMechanismGenerator/RMG-Py' }} run: | + echo ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ touch build/html/.nojekyll + echo ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ + touch build/html/AHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHH + echo ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ls -l + echo ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ pwd + echo ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ls -l build/html/ + echo ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ git status + echo ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ + git branch -vv + echo ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ cd build/html + echo ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ git status + echo ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ + git branch -vv + echo ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ git add -A . + echo ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ git status + echo ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ git commit -m "Automated documentation rebuild" + echo ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ git status + echo ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ git push --dry-run origin gh-pages + echo ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ From 5049aa9585c1768a0c2c10445f6f8da78ef0c7b4 Mon Sep 17 00:00:00 2001 From: Jackson Burns <33505528+JacksonBurns@users.noreply.github.com> Date: Thu, 29 Feb 2024 20:19:05 -0500 Subject: [PATCH 12/15] force add --- .github/workflows/docs.yml | 2 +- 1 file changed, 1 insertion(+), 1 deletion(-) diff --git a/.github/workflows/docs.yml b/.github/workflows/docs.yml index 01e8da461b..16e2f060f5 100644 --- a/.github/workflows/docs.yml +++ b/.github/workflows/docs.yml @@ -99,7 +99,7 @@ jobs: echo ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ git branch -vv echo ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ - git add -A . + git add --force -A . echo ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ git status echo ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ From 50f6513647ad6f363004654a273a67fb30717dee Mon Sep 17 00:00:00 2001 From: Jackson Burns <33505528+JacksonBurns@users.noreply.github.com> Date: Thu, 29 Feb 2024 22:16:28 -0500 Subject: [PATCH 13/15] try just manually force adding one of the changed files --- .github/workflows/docs.yml | 4 ++++ 1 file changed, 4 insertions(+) diff --git a/.github/workflows/docs.yml b/.github/workflows/docs.yml index 16e2f060f5..584a450c04 100644 --- a/.github/workflows/docs.yml +++ b/.github/workflows/docs.yml @@ -103,6 +103,10 @@ jobs: echo ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ git status echo ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ + git add --force -A build/html/latex-api.html + echo ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ + git status + echo ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ git commit -m "Automated documentation rebuild" echo ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ git status From 72e1e5532604eb3ccf726f53280c3ef6f70aabb6 Mon Sep 17 00:00:00 2001 From: Jackson Burns <33505528+JacksonBurns@users.noreply.github.com> Date: Fri, 1 Mar 2024 09:15:00 -0500 Subject: [PATCH 14/15] checkout complete history of RMG, also add test file correctly --- .github/workflows/docs.yml | 4 +++- 1 file changed, 3 insertions(+), 1 deletion(-) diff --git a/.github/workflows/docs.yml b/.github/workflows/docs.yml index 584a450c04..e720a67b45 100644 --- a/.github/workflows/docs.yml +++ b/.github/workflows/docs.yml @@ -16,6 +16,8 @@ jobs: shell: bash -l {0} steps: - uses: actions/checkout@v2 + with: + fetch-depth: 0 - name: Setup Mambaforge Python 3.7 uses: conda-incubator/setup-miniconda@v2 with: @@ -103,7 +105,7 @@ jobs: echo ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ git status echo ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ - git add --force -A build/html/latex-api.html + git add --force latex-api.html echo ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ git status echo ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ From c53434a7749b15425bfa08d09dcca1478ba9a21f Mon Sep 17 00:00:00 2001 From: Jackson Burns <33505528+JacksonBurns@users.noreply.github.com> Date: Fri, 1 Mar 2024 13:28:50 -0500 Subject: [PATCH 15/15] =?UTF-8?q?The=20FitnessGram=E2=84=A2=20Pacer=20Test?= =?UTF-8?q?=20is=20a=20multistage=20aerobic=20capacity=20test=20that=20pro?= =?UTF-8?q?gressively=20gets=20more=20difficult=20as=20it=20continues.=20T?= =?UTF-8?q?he=2020=20meter=20pacer=20test=20will=20begin=20in=2030=20secon?= =?UTF-8?q?ds.=20Line=20up=20at=20the=20start.=20The=20running=20speed=20s?= =?UTF-8?q?tarts=20slowly,=20but=20gets=20faster=20each=20minute=20after?= =?UTF-8?q?=20you=20hear=20this=20signal.=20[beep]=20A=20single=20lap=20sh?= =?UTF-8?q?ould=20be=20completed=20each=20time=20you=20hear=20this=20sound?= =?UTF-8?q?.=20[ding]=20Remember=20to=20run=20in=20a=20straight=20line,=20?= =?UTF-8?q?and=20run=20as=20long=20as=20possible.=20The=20second=20time=20?= =?UTF-8?q?you=20fail=20to=20complete=20a=20lap=20before=20the=20sound,=20?= =?UTF-8?q?your=20test=20is=20over.=20The=20test=20will=20begin=20on=20the?= =?UTF-8?q?=20word=20start.=20On=20your=20mark,=20get=20ready,=20start.?= MIME-Version: 1.0 Content-Type: text/plain; charset=UTF-8 Content-Transfer-Encoding: 8bit --- .github/workflows/docs.yml | 10 +++++++++- 1 file changed, 9 insertions(+), 1 deletion(-) diff --git a/.github/workflows/docs.yml b/.github/workflows/docs.yml index e720a67b45..c10f90abb2 100644 --- a/.github/workflows/docs.yml +++ b/.github/workflows/docs.yml @@ -49,7 +49,7 @@ jobs: with: ref: gh-pages clean: false - path: build/html + path: documentation/build/html fetch-depth: 0 # checkout the complete git history so upstream is seen as out of date when attempting to push these updates - name: Make documentation - for testing if: ${{ github.event_name != 'push' || github.repository != 'ReactionMechanismGenerator/RMG-Py' }} @@ -80,6 +80,14 @@ jobs: - name: Publish documentation # if: ${{ github.event_name == 'push' && github.repository == 'ReactionMechanismGenerator/RMG-Py' }} run: | + cd documentation/build/html + git add -A . + git commit -m "Automated documentation rebuild" + echo ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ + git status + echo ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ + git push --dry-run origin gh-pages + echo "THIS NEXT ONE SHOULD FAIL BECAUSE THAT DIR SHOULD NOT EXIST ANYMORE SINCE WE AREN'T CLONING GH-PAGES INTO IT" echo ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ touch build/html/.nojekyll echo ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~