From 33cc9eeb456cdf0c8d283d84875b484fbacb35c1 Mon Sep 17 00:00:00 2001 From: Jeffrey Curtis Date: Thu, 25 Sep 2025 16:14:18 -0500 Subject: [PATCH 1/7] first pass at doxygen for gh-pages --- .github/workflows/doxygen.yml | 21 +++++++++++++++++++++ doc/Doxyfile | 6 +++--- 2 files changed, 24 insertions(+), 3 deletions(-) create mode 100644 .github/workflows/doxygen.yml diff --git a/.github/workflows/doxygen.yml b/.github/workflows/doxygen.yml new file mode 100644 index 000000000..3c3a17be5 --- /dev/null +++ b/.github/workflows/doxygen.yml @@ -0,0 +1,21 @@ +name: Deploy Doxygen Docs + +on: + push: + branches: [doxygen] + +jobs: + deploy: + runs-on: ubuntu-latest + permissions: + contents: write + + steps: + - uses: actions/checkout@v3 + - name: Generate and Deploy Doxygen Docs + uses: DenverCoder1/doxygen-github-pages-action@v2.0.0 + with: + github_token: ${{ secrets.GITHUB_TOKEN }} + config_file: doc/Doxyfile + folder: html + branch: gh-pages diff --git a/doc/Doxyfile b/doc/Doxyfile index ac2191a14..895152879 100644 --- a/doc/Doxyfile +++ b/doc/Doxyfile @@ -844,7 +844,7 @@ WARN_LOGFILE = # spaces. See also FILE_PATTERNS and EXTENSION_MAPPING # Note: If this tag is empty the current directory is searched. -INPUT = ../src +INPUT = README.md src # This tag can be used to specify the character encoding of the source files # that doxygen parses. Internally doxygen uses the UTF-8 encoding. Doxygen uses @@ -1023,7 +1023,7 @@ FILTER_SOURCE_PATTERNS = # (index.html). This can be useful if you have a project on for instance GitHub # and want to reuse the introduction page also for the doxygen output. -USE_MDFILE_AS_MAINPAGE = +USE_MDFILE_AS_MAINPAGE = README.md #--------------------------------------------------------------------------- # Configuration options related to source browsing @@ -1221,7 +1221,7 @@ HTML_HEADER = # that doxygen normally uses. # This tag requires that the tag GENERATE_HTML is set to YES. -HTML_FOOTER = doxygen_footer.html +HTML_FOOTER = doc/doxygen_footer.html # The HTML_STYLESHEET tag can be used to specify a user-defined cascading style # sheet that is used by each HTML page. It can be used to fine-tune the look of From 6f4ffcae0a2600b3de2bd978d7981e3bd81071dd Mon Sep 17 00:00:00 2001 From: Jeffrey Curtis Date: Mon, 6 Oct 2025 20:56:16 -0500 Subject: [PATCH 2/7] remove doxygen workflow. combine upload in doc workflow --- .github/workflows/doc.yml | 22 ++++++++++++++++++++-- .github/workflows/doxygen.yml | 21 --------------------- 2 files changed, 20 insertions(+), 23 deletions(-) delete mode 100644 .github/workflows/doxygen.yml diff --git a/.github/workflows/doc.yml b/.github/workflows/doc.yml index b2503c3c5..be9795679 100644 --- a/.github/workflows/doc.yml +++ b/.github/workflows/doc.yml @@ -1,13 +1,31 @@ name: CI -on: [push, pull_request] +on: + push: + branches: [doxygen] jobs: build: runs-on: ubuntu-latest + permissions: + contents: write + steps: - - uses: actions/checkout@v1 + - uses: actions/checkout@v3 - name: Build the testing docker image run: docker build -t partmc-doc -f Dockerfile.doc . + - name: Run container to generate docs + run: docker run --name partmc-doc-container partmc-doc + - name: Create docs directory + run: mkdir -p doc + - name: Copy docs from container to local workspace + run: docker cp partmc-doc-container:/partmc/doc/html ./doc/html + - name: Deploy to GitHub Pages + uses: JamesIves/github-pages-deploy-action@v4 + with: + branch: gh-pages + folder: doc/html + - name: Clean up container + run: docker rm partmc-doc-container diff --git a/.github/workflows/doxygen.yml b/.github/workflows/doxygen.yml deleted file mode 100644 index 3c3a17be5..000000000 --- a/.github/workflows/doxygen.yml +++ /dev/null @@ -1,21 +0,0 @@ -name: Deploy Doxygen Docs - -on: - push: - branches: [doxygen] - -jobs: - deploy: - runs-on: ubuntu-latest - permissions: - contents: write - - steps: - - uses: actions/checkout@v3 - - name: Generate and Deploy Doxygen Docs - uses: DenverCoder1/doxygen-github-pages-action@v2.0.0 - with: - github_token: ${{ secrets.GITHUB_TOKEN }} - config_file: doc/Doxyfile - folder: html - branch: gh-pages From 51abdf092d370db83d40cd8a63545e8cd29b9605 Mon Sep 17 00:00:00 2001 From: Jeffrey Curtis Date: Mon, 6 Oct 2025 20:58:31 -0500 Subject: [PATCH 3/7] fix paths in doxyfile --- doc/Doxyfile | 4 ++-- 1 file changed, 2 insertions(+), 2 deletions(-) diff --git a/doc/Doxyfile b/doc/Doxyfile index 895152879..ea50e2934 100644 --- a/doc/Doxyfile +++ b/doc/Doxyfile @@ -844,7 +844,7 @@ WARN_LOGFILE = # spaces. See also FILE_PATTERNS and EXTENSION_MAPPING # Note: If this tag is empty the current directory is searched. -INPUT = README.md src +INPUT = ../README.md ../src # This tag can be used to specify the character encoding of the source files # that doxygen parses. Internally doxygen uses the UTF-8 encoding. Doxygen uses @@ -1221,7 +1221,7 @@ HTML_HEADER = # that doxygen normally uses. # This tag requires that the tag GENERATE_HTML is set to YES. -HTML_FOOTER = doc/doxygen_footer.html +HTML_FOOTER = doxygen_footer.html # The HTML_STYLESHEET tag can be used to specify a user-defined cascading style # sheet that is used by each HTML page. It can be used to fine-tune the look of From c972da985f90ee7e1655ca1927c71445d452430f Mon Sep 17 00:00:00 2001 From: Jeffrey Curtis Date: Tue, 7 Oct 2025 15:42:00 -0500 Subject: [PATCH 4/7] change to push and PR. only deploy on push --- .github/workflows/doc.yml | 2 ++ .github/workflows/{tchem.yml => tchem.yml.temporarily_off} | 0 2 files changed, 2 insertions(+) rename .github/workflows/{tchem.yml => tchem.yml.temporarily_off} (100%) diff --git a/.github/workflows/doc.yml b/.github/workflows/doc.yml index be9795679..1f59565f2 100644 --- a/.github/workflows/doc.yml +++ b/.github/workflows/doc.yml @@ -3,6 +3,7 @@ name: CI on: push: branches: [doxygen] + pull_request: jobs: build: @@ -23,6 +24,7 @@ jobs: - name: Copy docs from container to local workspace run: docker cp partmc-doc-container:/partmc/doc/html ./doc/html - name: Deploy to GitHub Pages + if: github.event_name == 'push' uses: JamesIves/github-pages-deploy-action@v4 with: branch: gh-pages diff --git a/.github/workflows/tchem.yml b/.github/workflows/tchem.yml.temporarily_off similarity index 100% rename from .github/workflows/tchem.yml rename to .github/workflows/tchem.yml.temporarily_off From c20a8bb66251b70340b3ac5d768c2bce5cf64207 Mon Sep 17 00:00:00 2001 From: Jeffrey Curtis Date: Wed, 5 Nov 2025 21:50:10 -0600 Subject: [PATCH 5/7] minor edits to README --- README.md | 6 +++--- 1 file changed, 3 insertions(+), 3 deletions(-) diff --git a/README.md b/README.md index 1c265e406..dfdcc0dd5 100644 --- a/README.md +++ b/README.md @@ -3,14 +3,14 @@ PartMC: Particle-resolved Monte Carlo code for atmospheric aerosol simulation -[![Latest version](https://img.shields.io/github/tag/compdyn/partmc.svg?label=version)](https://github.com/compdyn/partmc/blob/master/ChangeLog.md) [![Docker build status](https://img.shields.io/docker/automated/compdyn/partmc.svg)](https://hub.docker.com/r/compdyn/partmc/builds/) [![Github Actions Status](https://github.com/compdyn/partmc/workflows/CI/badge.svg?branch=master)](https://github.com/compdyn/partmc/actions/workflows/main.yml) [![License](https://img.shields.io/github/license/compdyn/partmc.svg)](https://github.com/compdyn/partmc/blob/master/COPYING) [![DOI](https://zenodo.org/badge/24058992.svg)](https://zenodo.org/badge/latestdoi/24058992) +[![Latest version](https://img.shields.io/github/tag/compdyn/partmc.svg?label=version)](https://github.com/compdyn/partmc/blob/master/ChangeLog.md) [![Documentation](https://img.shields.io/badge/docs-GitHub%20Pages-blue)](https://compdyn.github.io/partmc/) [![Docker build status](https://img.shields.io/docker/automated/compdyn/partmc.svg)](https://hub.docker.com/r/compdyn/partmc/builds/) [![Github Actions Status](https://github.com/compdyn/partmc/workflows/CI/badge.svg?branch=master)](https://github.com/compdyn/partmc/actions/workflows/main.yml) [![License](https://img.shields.io/github/license/compdyn/partmc.svg)](https://github.com/compdyn/partmc/blob/master/COPYING) [![DOI](https://zenodo.org/badge/24058992.svg)](https://zenodo.org/badge/latestdoi/24058992) Version 2.8.0 Released 2024-02-23 -**Source:** +**Repository:** -**Homepage:** +**Documentation:** **Cite as:** M. West, N. Riemer, J. Curtis, M. Michelotti, and J. Tian (2024) PartMC, [![version](https://img.shields.io/github/release/compdyn/partmc.svg?label=version)](https://github.com/compdyn/partmc), [![DOI](https://zenodo.org/badge/24058992.svg)](https://zenodo.org/badge/latestdoi/24058992) From 02bbdd359fee58990dab68e166f5bfd88c58af89 Mon Sep 17 00:00:00 2001 From: Jeffrey Curtis Date: Wed, 5 Nov 2025 22:20:07 -0600 Subject: [PATCH 6/7] add relative path for README to avoid issues --- doc/Doxyfile | 3 ++- 1 file changed, 2 insertions(+), 1 deletion(-) diff --git a/doc/Doxyfile b/doc/Doxyfile index ea50e2934..88f0b8654 100644 --- a/doc/Doxyfile +++ b/doc/Doxyfile @@ -895,6 +895,7 @@ FILE_PATTERNS = *.c \ *.php3 \ *.inc \ *.m \ + *.md \ *.mm \ *.dox \ *.py \ @@ -1023,7 +1024,7 @@ FILTER_SOURCE_PATTERNS = # (index.html). This can be useful if you have a project on for instance GitHub # and want to reuse the introduction page also for the doxygen output. -USE_MDFILE_AS_MAINPAGE = README.md +USE_MDFILE_AS_MAINPAGE = ../README.md #--------------------------------------------------------------------------- # Configuration options related to source browsing From fd642f8dd1b6c57acf4729b83eb50e712d94b9e1 Mon Sep 17 00:00:00 2001 From: Jeffrey Curtis Date: Wed, 5 Nov 2025 22:25:43 -0600 Subject: [PATCH 7/7] change name of workflow --- .github/workflows/doc.yml | 2 +- 1 file changed, 1 insertion(+), 1 deletion(-) diff --git a/.github/workflows/doc.yml b/.github/workflows/doc.yml index 1f59565f2..e7f8f36e0 100644 --- a/.github/workflows/doc.yml +++ b/.github/workflows/doc.yml @@ -1,4 +1,4 @@ -name: CI +name: Doxygen Build and Deploy on: push: