Update tex files

.github/workflows/ci.yml

@@ -20,8 +20,8 @@ name: AtChem2 CI
 # Controls when the workflow is activated
 on:
 
-  # Triggers when a pull request is created or updated (only on the
-  # master branch)
+  # Triggers when a pull request targeting the master branch is
+  # created or updated
   pull_request:
     branches: [ master ]
 
@@ -44,7 +44,7 @@ jobs:
     # here: https://github.com/actions/runner-images
     runs-on: ${{ matrix.os }}
     strategy:
-      matrix:
+      matrix: # macos testing temporarily deactivated
         os: [ubuntu-20.04, ubuntu-22.04] #, macos-12, macos-13]
         fortran: [10, 11, 12]
         exclude: # gfortran-11, gfortran-12 not available for ubuntu-20.04

.github/workflows/tex.yml

@@ -17,31 +17,27 @@ name: AtChem2 PDF
 # Controls when the workflow is activated
 on:
 
-  # Triggers when a pull request is created or updated (only on the
-  # master branch), and the .tex/.svg files modified
-  pull_request:
-    branches: [ master ]
-#    paths:
-#      - './doc/latex/*.tex'
-#      - './doc/figures/*.svg'
-
   # Triggers when a push is made to the master branch (either by
-  # merging a pull request, or by direct commit)
-#  push:
-#    branches: [ master ]
+  # merging a pull request, or by direct commit), and when any of the
+  # .tex/.svg files in `doc/` have been modified
+  push:
+    branches: [ master ]
+    paths:
+      - './doc/latex/*.tex'
+      - './doc/figures/*.svg'
 
   # Run manually from the Actions tab
-#  workflow_dispatch:
+  workflow_dispatch:
 
 # ------------------------------ JOBS ------------------------------ #
-# This workflow contains a single job called `pdf_manual` which sets
-# up a full TeXLive environment, compiles the source files, and
-# generates the pdf file of the manual
+# This workflow contains a single job called `pdf_manual` which runs
+# the script `make_manual_pdf.sh` to generate the pdf file of the
+# manual, and uploads it to the repo
 jobs:
   pdf_manual:
-    # The job runs on the latest version of linux (ubuntu)
+    # The job runs on the latest version of linux (ubuntu), and needs
+    # write permission to the repository
     runs-on: ubuntu-latest
-
     permissions:
       contents: write
 
@@ -52,23 +48,17 @@ jobs:
       - name: Checkout repo
         uses: actions/checkout@v4 # https://github.com/marketplace/actions/checkout
         with:
-#          fetch-depth: 2
-          ref: ${{ github.head_ref }}
+          ref: ${{ github.ref }}
 
-      - name: Check Token Permissions
-        run: |
-          echo "Token Permissions: $(curl -sSL -H "Authorization: Bearer ${{ secrets.GITHUB_TOKEN }}" \
-          https://api.github.com/repos/${{ github.repository }} | jq .permissions)"
-
-      # # -------------------------------------------------------------
-      # # 2. Setup TeXLive and Inkscape (v1.x), then run the script `make_manual_pdf.sh`
-      # - name: Setup TexLive and compile the manual
-      #   uses: xu-cheng/texlive-action@v2 # https://github.com/marketplace/actions/github-action-with-texlive
-      #   with:
-      #     scheme: full
-      #     run: |
-      #       apk add inkscape
-      #       ./tools/make_manual_pdf.sh
+      # -------------------------------------------------------------
+      # 2. Setup TeXLive, install Inkscape (v1.x), and compile the pdf file
+      - name: Setup TexLive and compile the manual
+        uses: xu-cheng/texlive-action@v2 # https://github.com/marketplace/actions/github-action-with-texlive
+        with:
+          scheme: full
+          run: |
+            apk add inkscape
+            ./tools/make_manual_pdf.sh
 
       # # -------------------------------------------------------------
       # # 3.
@@ -78,16 +68,16 @@ jobs:
       #     name: AtChem2-Manual.pdf
       #     path: doc/AtChem2-Manual.pdf
 
-      # # -------------------------------------------------------------
-      # # 4.
-      # - name: Add pdf to PR
-      #   env:
-      #     GITHUB_TOKEN: ${{ secrets.GITHUB_TOKEN }}
-      #   run: |
-      #     # configure git
-      #     git config --local user.name "github-actions[bot]"
-      #     git config --local user.email "github-actions[bot]@users.noreply.github.com"
-      #     # commit pdf file
-      #     git add doc/AtChem2-Manual.pdf
-      #     git commit -m "Update AtChem2-Manual.pdf"
-      #     git push origin HEAD:${{ github.ref }}
+      # -------------------------------------------------------------
+      # 4.
+      - name: Add pdf
+        env:
+          GITHUB_TOKEN: ${{ secrets.GITHUB_TOKEN }}
+        run: |
+          # configure git
+          git config --local user.name "github-actions[bot]"
+          git config --local user.email "github-actions[bot]@users.noreply.github.com"
+          # commit pdf file
+          git add doc/AtChem2-Manual.pdf
+          git commit -m "Update AtChem2-Manual.pdf"
+          #git push origin master

README.md

@@ -44,49 +44,3 @@ Set the initial conditions, the required outputs and the other model parameters
 The `atchem2` executable accepts several command line arguments to customize the location of the configuration, input and output directories, and of the shared library. More information on AtChem2, and detailed instructions on its installation, configuration and use can be found in the manual (`doc/AtChem2-Manual.pdf`) and in the GMD paper (see `CITATION.md`).
 
 The [AtChem2 wiki](https://github.com/AtChem/AtChem2/wiki) contains a summary of the instructions to install, compile, run and contribute to the development of Atchem2, together with additional information and a list of [known issues](https://github.com/AtChem/AtChem2/wiki/Known-Issues) with the suggested solutions or workarounds.
-
-
-Docker Container 
----------------------------------
-
-A containerised version of `AtChem2` is available. Currently this is built for release 1.2.2. The container is built on Rocky Linux 8.9 and pre-installs the `cvode` and `openlibm` dependencies via their relevant `tools/install/install_*.sh` scripts.
-
-The image can be downloaded via:
-
-```
-docker pull ghcr.io/wacl-york/atchem2:1.2.2
-```
-
-When running the container, changes to the model (e.g. those made to configurations, constraints and mechanisms) should be in a folder that matches the AtChem2 directory structure. This folder is then mounted as a volume to the container with the name `/data_transfer/`. The mechanism to use is provided as a positional argument to the image e.g. `./model/my_mech.fac`.
-
-#### Example host file structure:
-```
-my_model_run
-└── model
-    ├── configuration
-    ├── constraints
-    └── my_mech.fac
-```
-
-#### Example Docker run command:
-
-```
-docker run -it --rm -v /path/to/my_model_run:/data_transfer ghcr.io/wacl-york/atchem2:1.2.2 ./model/my_mech.fac
-```
-
-Outputs will be copied to `my_model_run/model/output` on completion.
-
-#### Running on Singularity / Apptainer
-
-Some HPC systems use Singularity / Apptainer instead of Docker as their container engine. This image is compatible with those aswell. The image can be converted to a .sif via:
-
-```
-apptainer pull path/to/image/atchem2.sif docker://ghcr.io/wacl-york/atchem2:1.2.2
-```
-#### Example Apptainer run command:
-
-```
-apptainer run --bind /path/to/my_model_run/:/data_transfer/ path/to/image/atchem2.sif ./model/my_mech.fac
-```
-> [!Note]
-> The leading "/" is important when mounting the volume for apptainer, as the container opens in the users "~" directory whereas Docker opens at "/"

doc/latex/Credits.tex

@@ -36,7 +36,7 @@ \section{Credits} \label{sec:credits}
 \item Marios Panagi
 \end{itemize}
 
-AtChem2 is a development of \href{https://atchem.york.ac.uk/}{AtChem-online},
+AtChem2 is a development of \href{https://atchem.york.ac.uk}{AtChem-online},
 which was created at the University of Leeds (and is now hosted at the
 University of York) by: