Migrate to pixi for development #57

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DunklesArchipel wants to merge 9 commits into IUPAC:main from DunklesArchipel:pixi

.gitattributes

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		@@ -0,0 +1,2 @@
		# SCM syntax highlighting & preventing 3-way merges
		pixi.lock merge=binary linguist-language=YAML linguist-generated=true

.github/workflows/deploy.yml

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+Diff line change
@@ Expand Up / @@ -5,32 +5,30 @@ on: @@
       push:
         branches:
         - main
+      pull_request:
+        types:
+          - opened
+          - synchronize
+          - reopened
     # This job installs dependencies, builds the book, and pushes it to `gh-pages`
     jobs:
       deploy-book:
         runs-on: ubuntu-latest
         steps:
-        - uses: actions/checkout@v3
+          - name: checkout
+            uses: actions/checkout@v6
+            with: { submodules: recursive }
+          - uses: prefix-dev/setup-pixi@v0.9.3
+            with: { pixi-version: v0.63.1 }
+          - name: Build the book
+            run: |
+              cd book
+              pixi run -e dev jupyter-book build
-        # Install dependencies
-        - name: Set up Python 3.11
-          uses: actions/setup-python@v4
-          with:
-            python-version: 3.11
-        - name: Install dependencies
-          run: |
-            pip install -r requirements.txt
-        # Build the book
-        - name: Build the book
-          run: |
-            jupyter-book build book
-        # Push the book's HTML to github-pages
-        - name: GitHub Pages action
-          uses: peaceiris/actions-gh-pages@v3.9.3
-          with:
-            github_token: ${{ secrets.GITHUB_TOKEN }}
-            publish_dir: book/_build/html
+          # Push the book's HTML to github-pages
+          - name: GitHub Pages action
+            uses: peaceiris/actions-gh-pages@v3.9.3
+            with:
+              github_token: ${{ secrets.GITHUB_TOKEN }}
+              publish_dir: book/_build/html

.gitignore

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+Diff line change
@@ -1,7 +1,24 @@
     .idea
     .DS_Store
-    book/_build
     book/manipulations/hiddensettings.py
     book/howtos/inchikeys.md
     book/.DS_Store
+    book/nul
     Pipfile.lock
+    # generated data from tests and builds
+    book/usecases/uvvis_metadata.png
+    book/_build
+    book/conformer1.txt
+    book/conformer2.txt
+    book/manipulations/.excel_import.md.bak
+    # pixi environments
+    .pixi/*
+    !.pixi/config.toml
+    # MyST build outputs
+    _build
+    # Jupyter Notebook
+    .ipynb_checkpoints

CONTRIBUTING.md

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@@ Expand Up / @@ -2,10 +2,73 @@ @@
     We welcome all community contributions to this work, whether it be a minor typo correction or a complex demonstration notebook.  There are a variety of ways you can help improve this resource, including:
-    # Issues
+    ## Issues
     If you spot something wrong or missing, please let us know through an [issue](https://github.com/IUPAC/WFChemCookbook/issues).  No coding required.  Just drop a line so we can follow up and make sure the resource is even better for the next person who comes along.
-    # Pull Requests
+    ## Pull Requests
-    More advanced practitioners should consider putting together a [pull request](https://github.com/IUPAC/WFChemCookbook/pulls).  Direct contributions are the fastest way to improve this work, whether it be because there's a quick editorial improvement or because we're missing the latest, greatest library.
+    More advanced practitioners should consider putting together a [pull request](https://github.com/IUPAC/WFChemCookbook/pulls).  Direct contributions are the fastest way to improve this work, whether it be because there's a quick editorial improvement or because we're missing the latest, greatest library.
+    ## Installation
+    This project can be downloaded directly from the repository website or via
+    ```sh .noeval
+    git clone git@github.com:IUPAC/WFChemCookbook.git
+    ```
+    Install [pixi](https://pixi.prefix.dev/dev/installation/) and install the dependencies via pixi.
+    ```sh .noeval
+    pixi install
+    ```
+    To explore the cookbook locally run:
+    ```sh .noeval
+    pixi run serve
+    ```
+    ### Further pixi tasks
+    Add a module:
+    ```sh .noeval
+    pixi add <module name>
+    ```
+    or
+    ```sh .noeval
+    pixi add --pypi <module name>
+    ```
+    Install packages
+    ```sh .noeval
+    pixi run install
+    ```
+    Clean cached packages
+    ```sh .noeval
+    pixi run clean
+    ```
+    Build the website (without serving) and check for broken links
+    ```sh .noeval
+    pixi run build
+    ```
+    If nothing works it is sometimes helpful to delete the `pixi.lock` file and clean the `.pixi` folder
+    The cache of the jupyter book build can be cleared (deletes `book/_build` folder)
+    TODO:: The build option "should" execute the notebooks and raise errors. This does not seem to work properly.
+    In addition the validity of links is checked.
+    ```sh .noeval
+    pixi run execute
+    ```

Pipfile

This file was deleted.

README.md

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@@ -1,4 +1,5 @@
     # IUPAC FAIR Chemistry Cookbook
     The IUPAC FAIR Chemistry Cookbook is an open, collaborate, community focused resource on how to work with FAIR data in chemistry.
     FAIR means findable, accessible, interoperable, and reusable and is the new paradigm for how chemists should share their data.
@@ Expand All @@
     The contents of this repository are designed to use the [Jupyter Book](https://jupyterbook.org/) framework to generate a simple to navigate and easy to maintain set of reference materials for getting started leveraging common and powerful chemical information tooling.
-    ## Developer instructions
-    See the [contributing guide](./CONTRIBUTING.md).
     ## About this project
     The Committee on Data of the International Science Council ([CODATA](https://codata.org/)) and the Research Data Alliance ([RDA](https://rd-alliance.org/)) have recently launched the [WorldFAIR Initiative](https://worldfair-project.eu/) to advance implementation of the [FAIR data principles](https://force11.org/info/the-fair-data-principles/) within and across research domains.
@@ Expand All @@
     General purpose software engineering strategies and techniques (_e.g._, Python language semantics, branch management in Git) are out of scope for this reference material, but an effort will be made to reference relevant external materials.
     *WorldFAIR “Global cooperation on FAIR data policy and practice” is funded by the EC HORIZON-WIDERA-2021-ERA-01-41 Coordination and Support Action under Grant Agreement No. 101058393.*
+    ## Contributing
+    See the [contributing guide](./CONTRIBUTING.md) with further information on how to contribute to this project, as wells as installation and development instructions.
+    ## Installation
+    This project can be downloaded directly from the repository website or via
+    ```sh .noeval
+    git clone git@github.com:theoechem/article_MAHE_2024_IL_pitfalls.git
+    ```
+    Install [pixi](https://pixi.prefix.dev/dev/installation/) and install the dependencies via pixi.
+    ```sh .noeval
+    pixi install
+    ```
+    To explore the Jupyter notebooks in `book` interactively use your favorite IDE or start jupyter via:
+    ```sh .noeval
+    pixi run jupyter lab
+    ```

book/_config.yml

This file was deleted.

book/_toc.yml

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