Better dependency management for dev, standalone, and a Nomad install (…

…#50)

* Added a pip-compile locked requirements for devs

* Reverted nomad-lab install back

* Fixed missing astroid version

* cleanup + ease on dev reqs

* Added a relaxed requirements.txt for installation with Nomad

* Unrelaxed pyproject.toml dev reqs and reverted xarray to older version

* Allowed python3.7 and fixed dask[array] version

* Merge adapt-nexus-to-metainfo-changes and CI updates

* cleanup

* Brought in requirements.txt

* draft refactoring and reorganizing of nomad-parser-nexus, decide first how tests should finally before structured, then the tests and absolute paths in the ipynbs and code sections should be changed

* renaming tools; adding and fixing unit tests

* fix some linting issues

* addig reference data for testing nexus checker

* fixing linting issues; adding test reference file

* bringing Example  to front

* tested ipynb notebooks, added jupyterlab_h5web to the environment

* improved descriptions, and placed jupyterlab in pyproject toml, tested compiling a dev-requirements locally successfully

* updating readme.md as a result of testing

* Added nexus definitions to the module package

* fixing README files and the ipynb for APM

* use dataconverter alias from command line

* harmonising EM and MPES notebooks

* Updated YAML file

* Updated jupyter notebook for ellipsometry + DAT and YAML file

* Delete ELLIPSOMETRY.NeXus.READER.EXAMPLE.02.ipynb

* Delete test.yaml

* fix data file locations

Co-authored-by: Adam Fekete <[email protected]>
Co-authored-by: Adam Fekete <[email protected]>
Co-authored-by: kuehbachm <[email protected]>
Co-authored-by: sanbrock <[email protected]>
Co-authored-by: sanbrock <[email protected]>
Co-authored-by: Carola Emminger <[email protected]>
Co-authored-by: cmmngr <[email protected]>

.github/workflows/pylint.yml

@@ -16,21 +16,21 @@ jobs:
           git submodule sync --recursive
           git submodule update --init --recursive --jobs=4
           python -m pip install --upgrade pip
-          pip install nomad-lab==1.1.3 --extra-index-url https://gitlab.mpcdf.mpg.de/api/v4/projects/2187/packages/pypi/simple
-          if [ -f requirements.txt ]; then pip install -r requirements.txt; fi
-          pip install astroid==2.5.1
       - name: Install package
         run: |
-          python -m pip install .
+          python -m pip install --no-deps .
+      - name: Install dev requirements
+        run: |
+          python -m pip install -r dev-requirements.txt
       - name: pycodestyle
         run: |
-          python -m pycodestyle --ignore=E501,E701,E731 nexusparser tests --exclude=nexusparser/definitions
+          python -m pycodestyle --ignore=E501,E701,E731 nexusutils tests --exclude=nexusutils/definitions
       - name: pylint
         run: |
-          python -m pylint --load-plugins=pylint_mongoengine,nomad.metainfo.pylint_plugin nexusparser tests
+          python -m pylint nexusutils tests
       - name: mypy
         run: |
-          python -m mypy --ignore-missing-imports --follow-imports=silent --no-strict-optional --exclude='nexusparser/definitions/' tests
+          python -m mypy --ignore-missing-imports --follow-imports=silent --no-strict-optional nexusutils tests
       - name: Test with pytest
         if: ${{ always() }}
         run: |

.gitignore

@@ -1,7 +1,204 @@
+# https://github.com/github/gitignore/blob/main/Global/macOS.gitignore
+# General
+.DS_Store
+.AppleDouble
+.LSOverride
+
+# Icon must end with two \r
+Icon
+
+
+# Thumbnails
+._*
+
+# Files that might appear in the root of a volume
+.DocumentRevisions-V100
+.fseventsd
+.Spotlight-V100
+.TemporaryItems
+.Trashes
+.VolumeIcon.icns
+.com.apple.timemachine.donotpresent
+
+# Directories potentially created on remote AFP share
+.AppleDB
+.AppleDesktop
+Network Trash Folder
+Temporary Items
+.apdisk
+
+# https://github.com/github/gitignore/blob/main/Python.gitignore
+
+# Byte-compiled / optimized / DLL files
+__pycache__/
+*.py[cod]
+*$py.class
+
+# C extensions
+*.so
+
+# Distribution / packaging
+.Python
+build/
+develop-eggs/
+dist/
+downloads/
+eggs/
+.eggs/
+lib/
+lib64/
+parts/
+sdist/
+var/
+wheels/
+share/python-wheels/
+*.egg-info/
+.installed.cfg
+*.egg
+MANIFEST
+
+# PyInstaller
+#  Usually these files are written by a python script from a template
+#  before PyInstaller builds the exe, so as to inject date/other infos into it.
+*.manifest
+*.spec
+
+# Installer logs
+pip-log.txt
+pip-delete-this-directory.txt
+
+# Unit test / coverage reports
+htmlcov/
+.tox/
+.nox/
+.coverage
+.coverage.*
+.cache
+nosetests.xml
+coverage.xml
+*.cover
+*.py,cover
+.hypothesis/
+.pytest_cache/
+cover/
+
+# Translations
+*.mo
+*.pot
+
+# Django stuff:
+*.log
+local_settings.py
+db.sqlite3
+db.sqlite3-journal
+
+# Flask stuff:
+instance/
+.webassets-cache
+
+# Scrapy stuff:
+.scrapy
+
+# Sphinx documentation
+docs/_build/
+
+# PyBuilder
+.pybuilder/
+target/
+
+# Jupyter Notebook
+.ipynb_checkpoints
+
+# IPython
+profile_default/
+ipython_config.py
+
+# pyenv
+#   For a library or package, you might want to ignore these files since the code is
+#   intended to run in multiple environments; otherwise, check them in:
+# .python-version
+
+# pipenv
+#   According to pypa/pipenv#598, it is recommended to include Pipfile.lock in version control.
+#   However, in case of collaboration, if having platform-specific dependencies or dependencies
+#   having no cross-platform support, pipenv may install dependencies that don't work, or not
+#   install all needed dependencies.
+#Pipfile.lock
+
+# poetry
+#   Similar to Pipfile.lock, it is generally recommended to include poetry.lock in version control.
+#   This is especially recommended for binary packages to ensure reproducibility, and is more
+#   commonly ignored for libraries.
+#   https://python-poetry.org/docs/basic-usage/#commit-your-poetrylock-file-to-version-control
+#poetry.lock
+
+# pdm
+#   Similar to Pipfile.lock, it is generally recommended to include pdm.lock in version control.
+#pdm.lock
+#   pdm stores project-wide configurations in .pdm.toml, but it is recommended to not include it
+#   in version control.
+#   https://pdm.fming.dev/#use-with-ide
+.pdm.toml
+
+# PEP 582; used by e.g. github.com/David-OConnor/pyflow and github.com/pdm-project/pdm
+__pypackages__/
+
+# Celery stuff
+celerybeat-schedule
+celerybeat.pid
+
+# SageMath parsed files
+*.sage.py
+
+# Environments
+.env
+.venv
+env/
+venv/
+ENV/
+env.bak/
+venv.bak/
+
+# Spyder project settings
+.spyderproject
+.spyproject
+
+# Rope project settings
+.ropeproject
+
+# mkdocs documentation
+/site
+
+# mypy
+.mypy_cache/
+.dmypy.json
+dmypy.json
+
+# Pyre type checker
+.pyre/
+
+# pytype static type analyzer
+.pytype/
+
+# Cython debug symbols
+cython_debug/
+
+# PyCharm
+#  JetBrains specific template is maintained in a separate JetBrains.gitignore that can
+#  be found at https://github.com/github/gitignore/blob/main/Global/JetBrains.gitignore
+#  and can be added to the global gitignore or merged into this file.  For a more nuclear
+#  option (not recommended) you can uncomment the following to ignore the entire idea folder.
+#.idea/
+
+
+# Custom settings
+
 .mypy_cache/
 .pyenv
 *.pyc
 *.txt
+!requirements.txt
+!dev-requirements.txt
 build/
 nexusparser.egg-info/PKG-INFO
 .python-version

.gitmodules

@@ -1,3 +1,6 @@
-[submodule "nexusparser/definitions"]
-	path = nexusparser/definitions
+[submodule "nexusutils/definitions"]
+	path = nexusutils/definitions
+	url = https://github.com/FAIRmat-Experimental/nexus_definitions.git
+[submodule "nexusutils/nexus_definitions"]
+	path = nexusutils/definitions
 	url = https://github.com/FAIRmat-Experimental/nexus_definitions.git

.vscode/settings.json

@@ -20,7 +20,7 @@
     "python.linting.enabled": true,
     "python.linting.pylintArgs": [
         "--load-plugins=nomad.metainfo.pylint_plugin",
-        "nexusparser",
+        "nexusutils",
         "tests"
     ],
     "python.testing.pytestArgs": [