use plugin template with cookiecutter and cruft (#16)

Co-authored-by: lukaspie <lukaspie@github.com>

Author: lukaspie

.cruft.json

@@ -0,0 +1,36 @@
+{
+  "template": "git@github.com:FAIRmat-NFDI/pynxtools-plugin-template.git",
+  "commit": "fd28d9fbb5463af44d47d8cdee098f854f3751e6",
+  "context": {
+    "cookiecutter": {
+      "reader_name": "igor",
+      "supported_nxdl": "*",
+      "short_description": "pynxtools-igor is a pynxtools reader plugin for data stored with Wavemetrics Igor Pro",
+      "technique": "igor",
+      "reader_class": "IgorReader",
+      "author_name": "The NOMAD Authors",
+      "author_email": "fairmat@physik.hu-berlin.de",
+      "github_username": "",
+      "organization_name": "fairmat-nfdi",
+      "license": "Apache Software License 2.0",
+      "zenodo_record": "15083998",
+      "vscode_settings": true,
+      "include_nomad_app": false,
+      "include_nomad_example_upload": true,
+      "include_north_tools": false,
+      "north_tool_name": "igor",
+      "__package_name": "pynxtools-igor",
+      "__module_name": "pynxtools_igor",
+      "__nomad_example": "igor_example_upload_entry_point",
+      "__nomad_app": "igor_app_entry_point",
+      "__north_tool_entry_point": "igor_north_tool_entry_point",
+      "_copy_without_render": [
+        "*.html"
+      ],
+      "_template": "git@github.com:FAIRmat-NFDI/pynxtools-plugin-template.git",
+      "_commit": "fd28d9fbb5463af44d47d8cdee098f854f3751e6"
+    }
+  },
+  "directory": null,
+  "checkout": null
+}

.cspell/custom-dictionary.txt

@@ -38,12 +38,14 @@ inlinehilite
 ipynb
 kernelspec
 linenums
+lukaspie
 mainfile
 ndarray
 nxdl
 nxdls
 orcid
 pymdownx
 pynxtools
+rettigl
 superfences
 voigt

.github/workflows/mkdocs-deploy.yml

@@ -3,7 +3,7 @@ name: build_and_deploy_mkdocs
 on:
   push:
     branches:
-      - main  # Triggers deployment on push to the main branch
+      - main
 
 env:
   python-version: 3.12
@@ -42,4 +42,4 @@ jobs:
 
       - name: Build and Deploy
         run: |
-          mkdocs gh-deploy --force --remote-branch gh-pages
+          mkdocs gh-deploy --force --remote-branch gh-pages

.github/workflows/publish.yml

@@ -109,4 +109,4 @@ jobs:
           name: dist-artifacts
           path: dist/
       - name: Publish package distributions to PyPI
-        uses: pypa/gh-action-pypi-publish@release/v1
+        uses: pypa/gh-action-pypi-publish@release/v1

.github/workflows/pylint.yml

@@ -16,7 +16,6 @@ jobs:
           python-version: ${{ env.python-version }}
       - name: Install package and dev dependencies
         run: |
-          curl -LsSf https://astral.sh/uv/install.sh | sh
           uv pip install ".[dev]"
       - name: ruff check
         run: |

.github/workflows/pytest.yml

@@ -20,23 +20,24 @@ jobs:
         uses: astral-sh/setup-uv@v5
         with:
           python-version: ${{ matrix.python-version }}
-      - name: Install package and test dependencies
+      - name: Install nomad
+        run: |
+          uv pip install nomad-lab[infrastructure]@git+https://gitlab.mpcdf.mpg.de/nomad-lab/nomad-FAIR.git
+      - name: Install package and pynxtools master branch
         run: |
+          # Editable install is neccessary for coveralls to work
           uv pip install -e ".[dev]"
           uv pip install coverage coveralls
       - name: Install pynxtools master branch
         run: |
-          uv pip install pynxtools@git+https://github.com/FAIRmat-NFDI/pynxtools@master
-      - name: Install nomad
-        run: |
-          uv pip install nomad-lab[infrastructure]@git+https://gitlab.mpcdf.mpg.de/nomad-lab/nomad-FAIR.git
+          uv pip install pynxtools@git+https://github.com/FAIRmat-NFDI/pynxtools
       - name: Test with pytest
         run: |
           coverage run -m pytest -sv --show-capture=no tests
       - name: Submit to coveralls
         continue-on-error: true
-        if: "${{ matrix.python-version == '3.12'}}"
+        if: ${{ matrix.python-version == '3.12' }}
         env:
             GITHUB_TOKEN: ${{ secrets.GITHUB_TOKEN }}
         run: |
-            coveralls --service=github
+            coveralls --service=github

.gitignore

@@ -88,8 +88,6 @@ cover/
 
 # Django stuff:
 *.log
-!tests/data/dataconverter/readers/igor/Ref_nexus_igor.log
-!tests/data/nexus/Ref_nexus_test.log
 local_settings.py
 db.sqlite3
 db.sqlite3-journal
@@ -199,11 +197,8 @@ cython_debug/
 .pyenv
 *.pyc
 *.txt
-!requirements.txt
-!dev-requirements.txt
 build/
-nexusparser.egg-info/PKG-INFO
 .python-version
-!tests/data/Ref_nexus_mpes.log
+!.cspell/custom-dictionary.txt
 *.nxs
 *.entry

.pre-commit-config.yaml

@@ -1,31 +1,38 @@
 repos:
   - repo: https://github.com/astral-sh/ruff-pre-commit
-    # Ruff version.
-    rev: v0.12.0
+    rev: v0.15.0
     hooks:
-      # Run the formatter.
+      - id: ruff-check
+        files: ^(src/pynxtools_igor|tests)/.*\.py$
       - id: ruff-format
-      # Run the linter.
-      - id: ruff
+        files: ^(src/pynxtools_igor|tests)/.*\.py$
+
   - repo: https://github.com/pre-commit/mirrors-mypy
-    rev: v1.7.1
+    rev: v1.19.1
     hooks:
-      - id: mypy
+      - id: mypy # static type checking
+
   - repo: https://github.com/asottile/pyupgrade
-    rev: v2.37.3
+    rev: v3.21.1
     hooks:
-    -   id: pyupgrade
-        args: [--py36-plus]
-  - repo: https://github.com/asottile/add-trailing-comma
-    rev: v2.2.3
-    hooks:
-    -   id: add-trailing-comma
-        args: [--py36-plus]
+      - id: pyupgrade
+        args: [--py310-plus] # modernizes syntax for Python 3.6+
+
   - repo: https://github.com/kynan/nbstripout
-    rev: 0.6.0
+    rev: 0.9.0
     hooks:
-    -   id: nbstripout
+      - id: nbstripout # removes notebook outputs before committing
+
   - repo: https://github.com/streetsidesoftware/cspell-cli
-    rev: v6.31.1
+    rev: v9.6.0
     hooks:
-      - id: cspell
+      - id: cspell # spellchecking
+        pass_filenames: false
+        args:
+          - --config
+          - cspell.json
+          - README.md
+          - CITATION.cff
+          - docs/**/*
+          - src/pynxtools_igor/**/*.py
+          - tests/**/*.py

CITATION.cff

@@ -17,25 +17,30 @@ authors:
     orcid: 'https://orcid.org/0000-0001-9361-8333'
 
 doi: 10.5281/zenodo.15083998
-repository-code: 'https://github.com/FAIRmat-NFDI/pynxtools-igor'
+repository-code: https://github.com/FAIRmat-NFDI/pynxtools-igor
 url: https://zenodo.org/records/15083998
 keywords:
+  - NeXus
+  - pynxtools
+  - NOMAD
   - Wavemetrics
   - Igor Pro
-  - NOMAD
-  - pynxtools
-  - NeXus
 abstract:
-  pynxtools-igor is a free, and open-source data software for converting data stored 
+  pynxtools-igor is a free, and open-source data software for converting data stored
   with Wavemetrics [Igor Pro](https://www.wavemetrics.com/) into the [NeXus](https://www.nexusformat.org/) 
-  format. It is implemented as a plugin for [pynxtools](https://github.com/FAIRmat-NFDI/pynxtools) and 
-  allows to read, translate, and standardize data from Igor Pro binary waves and packed experiment files. 
-  Depending on the domain of data, pynxtools allows to ensure compliance with various NeXus application 
-  definitions.
+  format. pynxtools-igor is a reader plugin for pynxtools (https://github.com/FAIRmat-NFDI/pynxtools)
+  written in Python. It allows to read, translate, and standardize data from Igor Pro binary waves and
+  packed experiment files. Depending on the domain of data, pynxtools-igor allows to ensure compliance with
+  various NeXus application definitions.
 
   pynxtools-igor is developed both as a standalone reader and as a tool within NOMAD, an open-source data
   management platform for materials science ((https://nomad-lab.eu/nomad-lab/).
 
   The work is funded by the Deutsche Forschungsgemeinschaft (DFG, German Research Foundation) - 460197019 (FAIRmat)
   (https://gepris.dfg.de/gepris/projekt/460197019?language=en).
-license: Apache-2.0
+license: Apache Software License 2.0
+funding:
+  - name: Deutsche Forschungsgemeinschaft
+    award-number: 460197019
+    title: FAIRmat - FAIR Data Infrastructure for Condensed-Matter Physics and the Chemical Physics of Solids
+    award-uri: https://gepris.dfg.de/gepris/projekt/460197019?language=en

MANIFEST.in

@@ -1,5 +1,5 @@
 prune *
 exclude *
 recursive-include src/pynxtools_igor *.py
-include pyproject.toml README.md dev-requirements.txt
-graft src/pynxtools_igor/nomad/examples
+include pyproject.toml README.md
+graft src/pynxtools_igor/nomad/example_uploads