diff --git a/.cspell/custom-dictionary.txt b/.cspell/custom-dictionary.txt index ff28973..bf46422 100644 --- a/.cspell/custom-dictionary.txt +++ b/.cspell/custom-dictionary.txt @@ -62,9 +62,11 @@ imwrite Interp ipykernel ipympl +ipynb ipython ipywidgets irfft +isin kernelspec kwds labview @@ -104,6 +106,7 @@ pcolormesh Phoibos polyfit polyval +pydata pyenv pygments pynxtools @@ -132,6 +135,7 @@ typehints TZCYXS undoc venv +viewcode vline vmax vmin diff --git a/.github/workflows/documentation.yml b/.github/workflows/documentation.yml index 2516397..1378f53 100644 --- a/.github/workflows/documentation.yml +++ b/.github/workflows/documentation.yml @@ -4,53 +4,46 @@ on: push: branches: [ main ] paths: - - specsanalyzer/**/* - - specsscan/**/* + - src/specsanalyzer/**/* + - src/specsscan/**/* - tutorial/** - .github/workflows/documentation.yml # Allows you to run this workflow manually from the Actions tab workflow_dispatch: - - # Sets permissions of the GITHUB_TOKEN to allow deployment to GitHub Pages -permissions: - contents: read - pages: write - id-token: write - -# Allow only one concurrent deployment, skipping runs queued between the run in-progress and latest queued. -# However, do NOT cancel in-progress runs as we want to allow these production deployments to complete. -concurrency: - group: "pages" - cancel-in-progress: false +env: + UV_SYSTEM_PYTHON: true jobs: build: runs-on: ubuntu-latest steps: - # Check out repo and set up Python - - name: Check out the repository - uses: actions/checkout@v4 + # Check out repo and set up Python + - uses: actions/checkout@v4 with: - lfs: true + fetch-depth: 0 # see https://stackoverflow.com/questions/57612428/cloning-private-github-repository-within-organisation-in-actions and https://docs.github.com/en/authentication/connecting-to-github-with-ssh/generating-a-new-ssh-key-and-adding-it-to-the-ssh-agent#generating-a-new-ssh-key - - name: checkout test data + - name: Fetch test data run: | eval `ssh-agent -s` ssh-add - <<< '${{ secrets.TEST_DATA_ACCESS_KEY }}' git submodule sync --recursive - git submodule update --init --recursive + git submodule update --init --recursive --jobs=4 - # Use cached python and dependencies, install poetry - - name: "Setup Python, Poetry and Dependencies" - uses: packetcoders/action-setup-cache-python-poetry@main + # Setup python + - name: Set up Python 3.10 + uses: actions/setup-python@v5 with: - python-version: 3.8 - poetry-version: 1.8.5 + python-version: "3.10" + + - name: Install dependencies + run: | + curl -LsSf https://astral.sh/uv/install.sh | sh - - name: Install notebook dependencies - run: poetry install -E notebook --with docs + - name: Install package + run: | + uv pip install ".[docs,notebook]" - name: Install pandoc run: | @@ -61,37 +54,80 @@ jobs: - name: copy tutorial files to docs run: | cp -r $GITHUB_WORKSPACE/tutorial $GITHUB_WORKSPACE/docs/ - cp -r $GITHUB_WORKSPACE/specsscan/config $GITHUB_WORKSPACE/docs/specsscan/ mkdir $GITHUB_WORKSPACE/docs/tests cp -r $GITHUB_WORKSPACE/tests/data $GITHUB_WORKSPACE/docs/tests/ - - # To be included later - # - name: Cache docs build - # id: cache-docs - # uses: actions/cache@v3 - # with: - # path: $GITHUB_WORKSPACE/_build - # key: ${{ runner.os }}-docs + mkdir -p $GITHUB_WORKSPACE/docs/src/specsscan + cp -r $GITHUB_WORKSPACE/src/specsscan/config $GITHUB_WORKSPACE/docs/src/specsscan - name: build Sphinx docs - run: poetry run sphinx-build -b html $GITHUB_WORKSPACE/docs $GITHUB_WORKSPACE/_build - - - name: Setup Pages - uses: actions/configure-pages@v3 + run: sphinx-build -b html $GITHUB_WORKSPACE/docs $GITHUB_WORKSPACE/_build - name: Upload artifact - uses: actions/upload-pages-artifact@v2 + uses: actions/upload-artifact@v4 with: - path: '_build' + name: sphinx-docs + path: _build - # Deployment job - deploy: - environment: - name: github-pages - url: ${{ steps.deployment.outputs.page_url }} + # this job pushes the built documentation to the docs repository + push: runs-on: ubuntu-latest needs: build steps: - - name: Deploy to GitHub Pages - id: deployment - uses: actions/deploy-pages@v2 + - name: Checkout docs repo + uses: actions/checkout@v2 + with: + repository: ${{ github.repository_owner }}/docs + token: ${{ secrets.GITHUB_TOKEN }} + path: 'docs-repo' + + - name: Set up Python 3.10 + uses: actions/setup-python@v5 + with: + python-version: "3.10" + + - name: Setup SSH + uses: webfactory/ssh-agent@v0.9.0 + with: + ssh-private-key: ${{ secrets.SSH_DOCS_DEPLOY_KEY }} + + - name: Download artifact + uses: actions/download-artifact@v4 + with: + name: sphinx-docs + path: sphinx-docs + + - name: Determine version folder + id: version-folder + run: | + if [[ $GITHUB_REF == refs/tags/* ]]; then + VERSION=${GITHUB_REF#refs/tags/} + echo "folder=specsanalyzer/$VERSION" >> $GITHUB_OUTPUT + rm docs-repo/specsanalyzer/stable + ln -s -r docs-repo/specsanalyzer/$VERSION docs-repo/specsanalyzer/stable + elif [[ $GITHUB_REF == refs/heads/main ]]; then + echo "folder=specsanalyzer/latest" >> $GITHUB_OUTPUT + else + echo "folder=specsanalyzer/develop" >> $GITHUB_OUTPUT + fi + + - name: Update switcher.json + run: | + VERSION=`grep "" sphinx-docs/index.html | sed -n 's/.*specsanalyzer \(.*\) documentation.*/\1/p'` + echo "python docs-repo/specsanalyzer/update_switcher.py docs-repo/specsanalyzer/switcher.json $GITHUB_REF $VERSION" + python docs-repo/specsanalyzer/update_switcher.py docs-repo/specsanalyzer/switcher.json $GITHUB_REF $VERSION + + - name: Copy documentation to the right version folder + run: | + mkdir -p docs-repo/${{ steps.version-folder.outputs.folder }} + cp -r sphinx-docs/* docs-repo/${{ steps.version-folder.outputs.folder }} + rm -rf docs-repo/${{ steps.version-folder.outputs.folder }}/.doctrees + rm -rf docs-repo/${{ steps.version-folder.outputs.folder }}/tutorial/*.ipynb + + - name: Push changes + run: | + cd docs-repo + git config user.name github-actions + git config user.email github-actions@github.com + git add . + git commit -m "Update documentation" + git push diff --git a/.github/workflows/linting.yml b/.github/workflows/linting.yml index bcd4693..3c1d864 100644 --- a/.github/workflows/linting.yml +++ b/.github/workflows/linting.yml @@ -6,42 +6,49 @@ on: paths-ignore: pyproject.toml +env: + UV_SYSTEM_PYTHON: true + jobs: lint: runs-on: ubuntu-latest steps: # Check out repo and set up Python - - uses: actions/checkout@v3 - with: - lfs: true + - uses: actions/checkout@v4 # see https://stackoverflow.com/questions/57612428/cloning-private-github-repository-within-organisation-in-actions and https://docs.github.com/en/authentication/connecting-to-github-with-ssh/generating-a-new-ssh-key-and-adding-it-to-the-ssh-agent#generating-a-new-ssh-key - - name: checkout test data + - name: Fetch test data run: | eval `ssh-agent -s` ssh-add - <<< '${{ secrets.TEST_DATA_ACCESS_KEY }}' git submodule sync --recursive - git submodule update --init --recursive + git submodule update --init --recursive --jobs=4 - # Use cached python and dependencies, install poetry - - name: "Setup Python, Poetry and Dependencies" - uses: packetcoders/action-setup-cache-python-poetry@main + # Setup python + - name: Set up Python 3.10 + uses: actions/setup-python@v5 with: - python-version: 3.8 - poetry-version: 1.8.5 + python-version: "3.10" + - name: Install dependencies + run: | + curl -LsSf https://astral.sh/uv/install.sh | sh + + - name: Install package + run: | + uv pip install ".[dev]" # Linting steps, execute all linters even if one fails - name: ruff run: - poetry run ruff specsanalyzer specsscan tests + ruff check src/specsanalyzer src/specsscan tests - name: ruff formatting if: ${{ always() }} run: - poetry run ruff format --check specsanalyzer specsscan tests + ruff format --check src/specsanalyzer src/specsscan tests - name: mypy if: ${{ always() }} run: - poetry run mypy specsanalyzer specsscan tests + mypy src/specsanalyzer src/specsscan tests - name: spellcheck if: ${{ always() }} uses: streetsidesoftware/cspell-action@v6 diff --git a/.github/workflows/release.yml b/.github/workflows/release.yml index 99cdb37..0a012aa 100644 --- a/.github/workflows/release.yml +++ b/.github/workflows/release.yml @@ -7,146 +7,40 @@ name: Publish to PyPI # Workflow does not trigger itself as it only changes pyproject.toml, which is not in paths for this workflow # The package is distributed as sed-processor on: - push: - branches: - - main - tags: - - v[0-9]+.[0-9]+.[0-9]+ - paths: - - specsanalyzer/**/* - - specsscan/**/* - - .github/workflows/release.yml + release: + types: [published] # Allows you to run this workflow manually from the Actions tab workflow_dispatch: jobs: - prerelease: - if: github.ref == 'refs/heads/main' - runs-on: ubuntu-latest - outputs: - version: ${{ steps.version.outputs.version }} - steps: - - uses: actions/checkout@v3 - with: - lfs: true - - - name: "Setup Python, Poetry and Dependencies" - uses: packetcoders/action-setup-cache-python-poetry@main - with: - python-version: 3.8 - poetry-version: 1.8.5 - - - name: bump pre-release version - id: version - working-directory: specsanalyzer - run: | - VERSION=$(poetry version -s prerelease) - echo "version=$VERSION" >> $GITHUB_OUTPUT - poetry build - - - name: Upload artifact - uses: actions/upload-artifact@v4 - with: - name: dist - path: dist - - - name: Upload pyproject.toml - uses: actions/upload-artifact@v4 - with: - name: pyproject - path: pyproject.toml - release: - if: startsWith(github.ref, 'refs/tags/') - runs-on: ubuntu-latest - outputs: - version: ${{ steps.version.outputs.version }} - steps: - - uses: actions/checkout@v3 - with: - lfs: true - - - name: "Setup Python, Poetry and Dependencies" - uses: packetcoders/action-setup-cache-python-poetry@main - with: - python-version: 3.8 - poetry-version: 1.8.5 - - - name: Bump release version and build - id: version - working-directory: specsanalyzer - run: | - VERSION=$(echo ${GITHUB_REF#refs/tags/v} | sed 's/-.*//') - echo "version=$VERSION" >> $GITHUB_OUTPUT - poetry version $VERSION - poetry build - - - name: Upload artifact - uses: actions/upload-artifact@v4 - with: - name: dist - path: dist - - - name: Upload pyproject.toml - uses: actions/upload-artifact@v4 - with: - name: pyproject - path: pyproject.toml - - publish: - needs: [prerelease, release] - if: always() && (needs.prerelease.result == 'success' || needs.release.result == 'success') + name: Upload release to PyPI runs-on: ubuntu-latest - outputs: - version: ${{ needs.prerelease.outputs.version || needs.release.outputs.version }} environment: - name: pypi - url: https://pypi.org/p/specsanalyzer + name: pypi + url: https://pypi.org/p/specsanalyzer permissions: - id-token: write + id-token: write steps: - - name: Download a single artifact - uses: actions/download-artifact@v4 + - uses: actions/checkout@v4 with: - name: dist + fetch-depth: 0 - - name: Publish package distributions to PyPI - uses: pypa/gh-action-pypi-publish@release/v1 + - name: Set up Python + uses: actions/setup-python@v5 with: - packages-dir: . + python-version: "3.x" - bump-version: - needs: publish - if: always() && (needs.publish.result == 'success') - runs-on: ubuntu-latest - steps: - - name: Generate a token - id: generate_token - uses: actions/create-github-app-token@v1 - with: - app-id: ${{ secrets.APP_ID }} - private-key: ${{ secrets.APP_PRIVATE_KEY }} - - - uses: actions/checkout@v3 - with: - lfs: true - token: ${{ steps.generate_token.outputs.token }} - - - name: Download pyproject.toml - uses: actions/download-artifact@v4 - with: - name: pyproject + - name: Install dependencies + run: | + curl -LsSf https://astral.sh/uv/install.sh | sh + uv pip install build - - name: Commit files + - name: Build package run: | - git config --local user.email "bump[bot]@users.noreply.github.com" - git config --local user.name "bump[bot]" - git add $GITHUB_WORKSPACE/pyproject.toml - git commit -m "bump version to ${{ needs.publish.outputs.version }}" + git reset --hard HEAD + python -m build - - name: Push changes - uses: ad-m/github-push-action@master - with: - github_token: ${{ steps.generate_token.outputs.token }} - branch: main + - name: Publish package distributions to PyPI + uses: pypa/gh-action-pypi-publish@release/v1 diff --git a/.github/workflows/testing_coverage.yml b/.github/workflows/testing_coverage.yml index 1a2baf9..a61f8e1 100644 --- a/.github/workflows/testing_coverage.yml +++ b/.github/workflows/testing_coverage.yml @@ -3,41 +3,49 @@ name: pytest and coverage report # Triggers the workflow on push for all branches and PR only for main on: push: + branches: [ main ] paths-ignore: pyproject.toml pull_request: branches: - main +env: + UV_SYSTEM_PYTHON: true + jobs: pytest: runs-on: ubuntu-latest steps: # Check out repo and set up Python - - name: Check out the repository - uses: actions/checkout@v4 - with: - lfs: true + - uses: actions/checkout@v4 # see https://stackoverflow.com/questions/57612428/cloning-private-github-repository-within-organisation-in-actions and https://docs.github.com/en/authentication/connecting-to-github-with-ssh/generating-a-new-ssh-key-and-adding-it-to-the-ssh-agent#generating-a-new-ssh-key - - name: checkout test data + - name: Fetch test data run: | eval `ssh-agent -s` ssh-add - <<< '${{ secrets.TEST_DATA_ACCESS_KEY }}' git submodule sync --recursive - git submodule update --init --recursive + git submodule update --init --recursive --jobs=4 - # Use cached python and dependencies, install poetry - - name: "Setup Python, Poetry and Dependencies" - uses: packetcoders/action-setup-cache-python-poetry@main + # Setup python + - name: Set up Python 3.10 + uses: actions/setup-python@v5 with: - python-version: 3.8 - poetry-version: 1.8.5 + python-version: "3.10" + + - name: Install dependencies + run: | + curl -LsSf https://astral.sh/uv/install.sh | sh + + - name: Install package + run: | + uv pip install ".[dev]" # Run pytest with coverage report, saving to xml - name: Run tests on python 3.8 run: | - poetry run pytest --cov --cov-report xml:cobertura.xml --full-trace --show-capture=no -sv -n auto tests/ + pytest --cov --cov-report xml:cobertura.xml --full-trace --show-capture=no -sv -n auto tests/ # Take report and upload to coveralls - name: Coveralls diff --git a/.github/workflows/testing_multiversion.yml b/.github/workflows/testing_multiversion.yml index e45d009..3b251ae 100644 --- a/.github/workflows/testing_multiversion.yml +++ b/.github/workflows/testing_multiversion.yml @@ -1,41 +1,52 @@ -name: unit tests [Python 3.8|3.9|3.10|3.11] +name: unit tests [multiversion] on: + schedule: + - cron: '0 1 * * 1' workflow_dispatch: push: branches: [ main ] paths-ignore: pyproject.toml +env: + UV_SYSTEM_PYTHON: true + jobs: pytest: + runs-on: ubuntu-latest # Using matrix strategy strategy: + fail-fast: false matrix: - python-version: ["3.8", "3.9", "3.10", "3.11"] - runs-on: ubuntu-latest + python-version: ["3.8", "3.9", "3.10", "3.11", "3.12"] + steps: # Check out repo and set up Python - - name: Check out the repository - uses: actions/checkout@v4 - with: - lfs: true + - uses: actions/checkout@v4 # see https://stackoverflow.com/questions/57612428/cloning-private-github-repository-within-organisation-in-actions and https://docs.github.com/en/authentication/connecting-to-github-with-ssh/generating-a-new-ssh-key-and-adding-it-to-the-ssh-agent#generating-a-new-ssh-key - - name: checkout test data + - name: Fetch test data run: | eval `ssh-agent -s` ssh-add - <<< '${{ secrets.TEST_DATA_ACCESS_KEY }}' git submodule sync --recursive - git submodule update --init --recursive + git submodule update --init --recursive --jobs=4 - - name: "Setup Python, Poetry and Dependencies" - uses: packetcoders/action-setup-cache-python-poetry@main + - name: Set up Python ${{ matrix.python-version }} + uses: actions/setup-python@v5 with: - python-version: ${{matrix.python-version}} - poetry-version: 1.8.5 + python-version: ${{ matrix.python-version }} + + - name: Install dependencies + run: | + curl -LsSf https://astral.sh/uv/install.sh | sh + + - name: Install package + run: | + uv pip install ".[dev]" # Use cached python and dependencies, install poetry - name: Run tests on python ${{matrix.python-version}} run: | - poetry run pytest --full-trace --show-capture=no -sv -n auto tests/ + pytest --full-trace --show-capture=no -sv -n auto tests/ diff --git a/.github/workflows/update_dependencies.yml b/.github/workflows/update_dependencies.yml deleted file mode 100644 index eeb8e8a..0000000 --- a/.github/workflows/update_dependencies.yml +++ /dev/null @@ -1,74 +0,0 @@ -name: Update dependencies in poetry lockfile - -on: - schedule: - - cron: '0 1 * * 1' - workflow_dispatch: - push: - branches: main - paths: - - .github/workflows/update_dependencies.yml - -jobs: - update_dependencies: - runs-on: ubuntu-latest - steps: - # Check out repo and set up Python - - uses: actions/checkout@v3 - with: - lfs: true - -# see https://stackoverflow.com/questions/57612428/cloning-private-github-repository-within-organisation-in-actions - - name: checkout test data - run: | - eval `ssh-agent -s` - ssh-add - <<< '${{ secrets.TEST_DATA_ACCESS_KEY }}' - git submodule sync --recursive - git submodule update --init --recursive - - -# see https://github.com/peter-evans/create-pull-request/blob/main/docs/concepts-guidelines.md - - uses: tibdex/github-app-token@v1 - id: generate-token - with: - app_id: ${{ secrets.APP_ID }} - private_key: ${{ secrets.APP_PRIVATE_KEY }} - - # Use cached python and dependencies, install poetry - - name: "Setup Python, Poetry and Dependencies" - uses: packetcoders/action-setup-cache-python-poetry@main - with: - python-version: 3.8 - poetry-version: 1.8.5 - - # update poetry lockfile - - name: "Update poetry lock file" - id: update - run: | - poetry self update - exec 5>&1 - UPDATE_OUTPUT=$(poetry update|tee >(cat - >&5)) - echo "UPDATE_OUTPUT<<EOF" >> $GITHUB_OUTPUT - echo "$UPDATE_OUTPUT" >> $GITHUB_OUTPUT - echo "EOF" >> $GITHUB_OUTPUT - - - name: Obtain git status - id: status - run: | - exec 5>&1 - STATUS=$(git status|tee >(cat - >&5)) - echo "STATUS<<EOF" >> $GITHUB_OUTPUT - echo "$STATUS" >> $GITHUB_OUTPUT - echo "EOF" >> $GITHUB_OUTPUT - - # create pull request if necessary - - name: "Create Pull Request" - uses: peter-evans/create-pull-request@v5 - if: ${{ contains(steps.status.outputs.STATUS, 'poetry.lock')}} - with: - token: ${{ steps.generate-token.outputs.token }} - commit-message: Update dependencies - title: "Update dependencies" - body: | - Dependency updates using Poetry: - ${{ steps.update.outputs.UPDATE_OUTPUT }} diff --git a/.gitignore b/.gitignore index 4a0e404..48ee5cd 100755 --- a/.gitignore +++ b/.gitignore @@ -140,5 +140,5 @@ dmypy.json *.nxs *.pxp -# poetry -poetry.toml +# installation +specsanalyzer.egg-info diff --git a/MANIFEST.in b/MANIFEST.in index f321f4c..0e9c7da 100644 --- a/MANIFEST.in +++ b/MANIFEST.in @@ -1,2 +1,7 @@ -include specsanalyzer/config/* -include specsscan/config/* +prune * +exclude * +recursive-include src/specsanalyzer *.py +recursive-include src/specsscan *.py +include pyproject.toml README.md +graft src/specsanalyzer/config/ +graft src/specsscan/config/ diff --git a/cspell.json b/cspell.json index bf7a020..ad92cb6 100644 --- a/cspell.json +++ b/cspell.json @@ -5,7 +5,8 @@ "*.toml", "Makefile", "*.bat", - "*.pxp" + "*.pxp", + "*.egg-info", ], "dictionaryDefinitions": [ { diff --git a/docs/conf.py b/docs/conf.py index 7352eb2..4044d97 100644 --- a/docs/conf.py +++ b/docs/conf.py @@ -13,6 +13,8 @@ import tomlkit +from specsanalyzer import __version__ + sys.path.insert(0, os.path.abspath("..")) @@ -23,7 +25,7 @@ def _get_project_meta(): with open("../pyproject.toml") as pyproject: file_contents = pyproject.read() - return tomlkit.parse(file_contents)["tool"]["poetry"] + return tomlkit.parse(file_contents)["project"] pkg_meta = _get_project_meta() @@ -32,7 +34,7 @@ def _get_project_meta(): author = "OpenCOMPES team" # The short X.Y version -version = str(pkg_meta["version"]) +version = __version__ # The full version, including alpha/beta/rc tags release = version @@ -42,13 +44,12 @@ def _get_project_meta(): # extensions coming with Sphinx (named 'sphinx.ext.*') or your custom # ones. extensions = [ - "sphinx_rtd_theme", "sphinx.ext.autodoc", "sphinx.ext.napoleon", "sphinx.ext.todo", "sphinx.ext.coverage", "sphinx.ext.autosummary", - "sphinx.ext.coverage", + "sphinx.ext.viewcode", "sphinx_autodoc_typehints", "nbsphinx", "myst_parser", @@ -89,7 +90,7 @@ def _get_project_meta(): # List of patterns, relative to source directory, that match files and # directories to ignore when looking for source files. # This pattern also affects html_static_path and html_extra_path. -exclude_patterns = ["_build", "Thumbs.db", ".DS_Store"] +exclude_patterns = ["_build", "Thumbs.db", ".DS_Store", "**.ipynb_checkpoints"] # -- Options for HTML output ------------------------------------------------- @@ -97,7 +98,28 @@ def _get_project_meta(): # The theme to use for HTML and HTML Help pages. See the documentation for # a list of builtin themes. # -html_theme = "sphinx_rtd_theme" +html_theme = "pydata_sphinx_theme" + +html_theme_options = { + "github_url": "https://github.com/OpenCOMPES/specsanalyzer", + "primary_sidebar_end": ["indices.html"], + "navbar_center": ["version-switcher", "navbar-nav"], + "show_nav_level": 2, + "show_version_warning_banner": True, + # maybe better to use _static/switcher.json on github pages link instead of the following + "switcher": { + "json_url": "https://raw.githubusercontent.com/OpenCOMPES/docs/main/specsanalyzer/switcher.json", + "version_match": version, + }, + "content_footer_items": ["last-updated"], +} + +html_context = { + "github_user": "OpenCOMPES", + "github_repo": "specsanalyzer", + "github_version": "main", + "doc_path": "docs", +} # Add any paths that contain custom static files (such as style sheets) here, # relative to this directory. They are copied after the builtin static files, diff --git a/docs/specsanalyzer/config.rst b/docs/specsanalyzer/config.rst index ab95c68..4165f69 100644 --- a/docs/specsanalyzer/config.rst +++ b/docs/specsanalyzer/config.rst @@ -23,17 +23,17 @@ API Default specsanalyzer configuration settings *************************************************** -.. literalinclude:: ../../specsanalyzer/config/default.yaml +.. literalinclude:: ../../src/specsanalyzer/config/default.yaml :language: yaml Default specsscan configuration settings *************************************************** -.. literalinclude:: ../../specsscan/config/default.yaml +.. literalinclude:: ../../src/specsscan/config/default.yaml :language: yaml Example configuration file for the trARPES setup at FHI-Berlin ********************************************************************************* -.. literalinclude:: ../../specsscan/config/example_config_FHI.yaml +.. literalinclude:: ../../src/specsscan/config/example_config_FHI.yaml :language: yaml diff --git a/poetry.lock b/poetry.lock deleted file mode 100644 index f2f7226..0000000 --- a/poetry.lock +++ /dev/null @@ -1,4350 +0,0 @@ -# This file is automatically @generated by Poetry 1.8.5 and should not be changed by hand. - 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{include = "specsanalyzer"}, - {include = "specsscan"}, +[build-system] +requires = ["setuptools>=64.0.1", "setuptools-scm[toml]>=6.2"] +build-backend = "setuptools.build_meta" + +[tool.setuptools.packages.find] +where = [ + "src", ] -version = "0.4.2a0" + +[tool.setuptools_scm] + +[project] +name = "specsanalyzer" +dynamic = ["version"] description = "Python package for loading and converting SPECS Phoibos analyzer data." authors = [ - "Laurenz Rettig <rettig@fhi-berlin.mpg.de>", - "Michele Puppin <michele.puppin@epfl.ch>", - "Abeer Arora <arora@fhi-berlin.mpg.de>", + {name = "Laurenz Rettig", email = "rettig@fhi-berlin.mpg.de"}, + {name = "Michele Puppin", email = "michele.puppin@epfl.ch"}, + {name = "Abeer Arora", email = "arora@fhi-berlin.mpg.de"}, ] readme = "README.md" -repository = "https://github.com/mpes-kit/specsanalyzer" -documentation = "https://github.com/mpes-kit/specsanalyzer/docs" -keywords=["specs", "phoibos", "arpes"] -license = "MIT" - -[tool.poetry.dependencies] -python = ">=3.8, <3.12" -docutils = "<0.21" -h5py = ">=3.6.0" -imutils = ">=0.5.4" -ipympl = ">=0.9.1" -ipywidgets = ">=7.7.1" -matplotlib = ">=3.5.1" -numpy = ">=1.21.6" -opencv-python = ">=4.8.1.78" -pynxtools-mpes = ">=0.2.0" -pynxtools = ">=0.7.0" -python-dateutil = ">=2.8.2" -pyyaml = ">=6.0" -xarray = ">=0.20.2" -tifffile = ">=2022.5.4" -tqdm = ">=4.62.3" -scipy = ">=1.8.0" -jupyter = {version = ">=1.0.0", extras = ["notebook"], optional = true} -ipykernel = {version = ">=6.9.1", extras = ["notebook"], optional = true} -jupyterlab-h5web = {version = ">=7.0.0", extras = ["notebook"], optional = true} - -[tool.poetry.extras] -notebook = ["jupyter", "ipykernel", "jupyterlab-h5web"] - -[tool.poetry.group.dev.dependencies] -pytest = ">=7.0.1" -pytest-cov = ">=3.0.0" -pytest-xdist = ">=2.5.0" -pytest-clarity = ">=1.0.1" -ruff = ">=0.1.7, <0.3.0" -mypy = ">=1.6.0, <1.10.0" -types-pyyaml = ">=6.0.12.12" -types-requests = ">=2.31.0.9" -pre-commit = ">=3.0.0" - -[tool.poetry.group.docs] -optional = true +keywords = ["specs", "phoibos", "arpes"] +license = {text = "MIT"} +requires-python = ">=3.8,<3.13" +dependencies = [ + "docutils<0.21", + "h5py>=3.6.0", + "imutils>=0.5.4", + "ipympl>=0.9.1", + "ipywidgets>=7.7.1", + "matplotlib>=3.5.1", + "numpy>=1.21.6", + "opencv-python>=4.8.1.78", + "pynxtools-mpes>=0.2.1", + "pynxtools>=0.9.3", + "python-dateutil>=2.8.2", + "pyyaml>=6.0", + "xarray>=0.20.2", + "tifffile>=2022.5.4", + "tqdm>=4.62.3", + "scipy>=1.8.0", +] -[tool.poetry.group.docs.dependencies] -sphinx = ">=7.1.2" -sphinx-rtd-theme = ">=1.0.0" -tomlkit = ">=0.12.0" -sphinx-autodoc-typehints = ">=1.17.0" -nbsphinx = ">=0.9.3" -myst-parser = ">=2.0.0" +[project.urls] +repository = "https://github.com/OpenCOMPES/specsanalyzer" +documentation = "https://opencompes.github.io/docs/specsanalyzer/latest/" -[build-system] -requires = ["poetry-core>=1.0.0"] -build-backend = "poetry.core.masonry.api" +[project.optional-dependencies] +dev = [ + "pytest>=7.0.1", + "pytest-cov>=3.0.0", + "pytest-xdist>=2.5.0", + "pytest-clarity>=1.0.1", + "ruff<0.3.0,>=0.1.7", + "mypy<1.10.0,>=1.6.0", + "types-pyyaml>=6.0.12.12", + "types-requests>=2.31.0.9", + "pre-commit>=3.0.0", +] +docs = [ + "sphinx>=7.1.2", + "tomlkit>=0.12.0", + "sphinx-autodoc-typehints>=1.17.0", + "nbsphinx>=0.9.3", + "myst-parser>=2.0.0", + "pydata-sphinx-theme>=0.15.0", +] +notebook = [ + "jupyter>=1.0.0", + "ipykernel>=6.9.1", + "jupyterlab>=4.0", + "jupyterlab-h5web>=7.0.0", +] [tool.coverage.report] omit = [ diff --git a/specsanalyzer/__init__.py b/src/specsanalyzer/__init__.py similarity index 59% rename from specsanalyzer/__init__.py rename to src/specsanalyzer/__init__.py index e6b114e..3ba370e 100755 --- a/specsanalyzer/__init__.py +++ b/src/specsanalyzer/__init__.py @@ -1,6 +1,8 @@ """SpecsAnalyzer class easy access APIs""" # Easy access APIs +import importlib.metadata + from .core import SpecsAnalyzer -__version__ = "0.1.0" +__version__ = importlib.metadata.version("specsanalyzer") __all__ = ["SpecsAnalyzer"] diff --git a/specsanalyzer/config.py b/src/specsanalyzer/config.py similarity index 100% rename from specsanalyzer/config.py rename to src/specsanalyzer/config.py diff --git a/specsanalyzer/config/default.yaml b/src/specsanalyzer/config/default.yaml similarity index 100% rename from specsanalyzer/config/default.yaml rename to src/specsanalyzer/config/default.yaml diff --git a/specsanalyzer/config/phoibos150.calib2d b/src/specsanalyzer/config/phoibos150.calib2d similarity index 100% rename from specsanalyzer/config/phoibos150.calib2d rename to src/specsanalyzer/config/phoibos150.calib2d diff --git a/specsanalyzer/convert.py b/src/specsanalyzer/convert.py similarity index 98% rename from specsanalyzer/convert.py rename to src/specsanalyzer/convert.py index e1173f0..aaa015f 100755 --- a/specsanalyzer/convert.py +++ b/src/specsanalyzer/convert.py @@ -91,7 +91,7 @@ def get_damatrix_from_calib2d( dims = ["Position", "Ekin"] else: - raise ValueError(f"Unrecognized lens mode '{lens_mode}") + raise ValueError(f"Unrecognized lens mode '{lens_mode}'") return a_inner, da_matrix, retardation_ratio, source, dims @@ -424,8 +424,8 @@ def calculate_matrix_correction( angle_axis = np.linspace(angle_low, angle_high, ny_pixels, endpoint=False) - mcp_position_mm_matrix = np.zeros([nx_pixels, ny_pixels]) - angular_correction_matrix = np.zeros([nx_pixels, ny_pixels]) + mcp_position_mm_matrix = np.zeros([nx_pixels, ny_pixels], dtype=float) + angular_correction_matrix = np.zeros([nx_pixels, ny_pixels], dtype=float) e_correction = np.zeros(ek_axis.shape) # create a meshgrid for vectorized evaluation diff --git a/specsanalyzer/core.py b/src/specsanalyzer/core.py similarity index 99% rename from specsanalyzer/core.py rename to src/specsanalyzer/core.py index 88f8406..c461bcf 100755 --- a/specsanalyzer/core.py +++ b/src/specsanalyzer/core.py @@ -495,10 +495,10 @@ def crop_tool( ) def update(hline, vline, v_vals): - lineh1.set_ydata(hline[0]) - lineh2.set_ydata(hline[1]) - linev1.set_xdata(vline[0]) - linev2.set_xdata(vline[1]) + lineh1.set_ydata([hline[0]]) + lineh2.set_ydata([hline[1]]) + linev1.set_xdata([vline[0]]) + linev2.set_xdata([vline[1]]) mesh_obj.set_clim(vmin=v_vals[0], vmax=v_vals[1]) fig.canvas.draw_idle() diff --git a/specsanalyzer/img_tools.py b/src/specsanalyzer/img_tools.py similarity index 100% rename from specsanalyzer/img_tools.py rename to src/specsanalyzer/img_tools.py diff --git a/specsanalyzer/io.py b/src/specsanalyzer/io.py similarity index 100% rename from specsanalyzer/io.py rename to src/specsanalyzer/io.py diff --git a/specsscan/__init__.py b/src/specsscan/__init__.py similarity index 56% rename from specsscan/__init__.py rename to src/specsscan/__init__.py index 4dc0f55..691e22c 100755 --- a/specsscan/__init__.py +++ b/src/specsscan/__init__.py @@ -1,6 +1,8 @@ """SpecsScan class easy access APIs""" # Easy access APIs +import importlib.metadata + from .core import SpecsScan -__version__ = "0.1.0" +__version__ = importlib.metadata.version("specsanalyzer") __all__ = ["SpecsScan"] diff --git a/specsscan/config/NXmpes_arpes_config.json b/src/specsscan/config/NXmpes_arpes_config.json similarity index 100% rename from specsscan/config/NXmpes_arpes_config.json rename to src/specsscan/config/NXmpes_arpes_config.json diff --git a/specsscan/config/default.yaml b/src/specsscan/config/default.yaml similarity index 100% rename from specsscan/config/default.yaml rename to src/specsscan/config/default.yaml diff --git a/specsscan/config/example_config_FHI.yaml b/src/specsscan/config/example_config_FHI.yaml similarity index 96% rename from specsscan/config/example_config_FHI.yaml rename to src/specsscan/config/example_config_FHI.yaml index d9f7193..5f5aec9 100644 --- a/specsscan/config/example_config_FHI.yaml +++ b/src/specsscan/config/example_config_FHI.yaml @@ -57,12 +57,12 @@ nexus: # the NeXus definition to use definition: "NXmpes_arpes" # additional input files, e.g. config and ELN files - input_files: ["../specsscan/config/NXmpes_arpes_config.json"] + input_files: ["../src/specsscan/config/NXmpes_arpes_config.json"] # parameters for the SpecsAnalyzer spa_params: # path to SPECS calib2d file (provided together with your analyzer) - calib2d_file: "../tests/data/phoibos150.calib2d" + calib2d_file: "../../tests/data/phoibos150.calib2d" # number of pixels along the energy dispersing direction nx_pixel: 1376 # number of pixels along the angle/spatially dispersing direction diff --git a/specsscan/core.py b/src/specsscan/core.py similarity index 99% rename from specsscan/core.py rename to src/specsscan/core.py index 8f12d1a..ee6e121 100755 --- a/specsscan/core.py +++ b/src/specsscan/core.py @@ -643,7 +643,7 @@ def process_sweep_scan( energy_indices = np.argwhere(energies.values).squeeze() # filling target array using "nearest" method target_energy = data.Ekin.sel(Ekin=converted.Ekin[energies > 0], method="nearest") - target_indices = np.argwhere(np.in1d(data.Ekin.values, target_energy.values)).squeeze() + target_indices = np.argwhere(np.isin(data.Ekin.values, target_energy.values)).squeeze() data[:, target_indices] += converted[:, energy_indices].values self.spa.print_msg = True diff --git a/specsscan/helpers.py b/src/specsscan/helpers.py similarity index 100% rename from specsscan/helpers.py rename to src/specsscan/helpers.py diff --git a/tests/data b/tests/data index aefc670..e921fe9 160000 --- a/tests/data +++ b/tests/data @@ -1 +1 @@ -Subproject commit aefc67081ffae66307a2d7b3f9adb29df809fda7 +Subproject commit e921fe9c198d263c900d8568476e12e4dcef82b8 diff --git a/tests/test_config.py b/tests/test_config.py index 0517a33..20742d0 100644 --- a/tests/test_config.py +++ b/tests/test_config.py @@ -1,7 +1,6 @@ """This is a code that performs several tests for the settings loader.""" import os import tempfile -from importlib.util import find_spec from pathlib import Path import pytest @@ -11,7 +10,7 @@ from specsanalyzer.config import parse_config from specsanalyzer.config import save_config -package_dir = os.path.dirname(find_spec("specsanalyzer").origin) +test_dir = os.path.dirname(__file__) default_config_keys = [ "calib2d_file", "nx_pixel", @@ -44,10 +43,10 @@ def test_load_dict(): def test_load_config(): """Test if the config loader can handle json and yaml files.""" config_json = load_config( - f"{package_dir}/../tests/data/config/config.json", + f"{test_dir}/data/config/config.json", ) config_yaml = load_config( - f"{package_dir}/../tests/data/config/config.yaml", + f"{test_dir}/data/config/config.yaml", ) assert config_json == config_yaml @@ -55,7 +54,7 @@ def test_load_config(): def test_load_config_raise(): """Test if the config loader raises an error for a wrong file type.""" with pytest.raises(TypeError): - load_config(f"{package_dir}/../README.md") + load_config(f"{test_dir}/../README.md") def test_complete_dictionary(): diff --git a/tests/test_convert.py b/tests/test_convert.py index 7bed600..6fac9ae 100755 --- a/tests/test_convert.py +++ b/tests/test_convert.py @@ -10,12 +10,7 @@ from specsanalyzer.convert import calculate_polynomial_coef_da from specsanalyzer.convert import get_damatrix_from_calib2d -package_dir = os.path.dirname(specsanalyzer.__file__) -test_dir = package_dir + "/../tests/data/" - -# from specsanalyzer.convert import get_rr_da -# from specsanalyzer.convert import mcp_position_mm -# let's get all the functions to be tested +test_dir = os.path.dirname(__file__) def test_da_matrix(): # pylint: disable=too-many-locals @@ -24,7 +19,7 @@ def test_da_matrix(): # pylint: disable=too-many-locals ######################################## # Load the IGOR txt Di_coeff values for comparison - igor_data_path = os.fspath(f"{test_dir}/dataEPFL/R9132") + igor_data_path = os.fspath(f"{test_dir}/data/dataEPFL/R9132") # get the Da coefficients di_file_list = [f"{igor_data_path}/Da{i}_value.tsv" for i in np.arange(1, 8, 2)] @@ -42,8 +37,9 @@ def test_da_matrix(): # pylint: disable=too-many-locals igor_d_coef_list.append(np.loadtxt(f_handle, delimiter="\t")) igor_d_coef_matrix = np.flip(np.vstack(igor_d_coef_list), axis=1) - config_path = os.fspath(f"{test_dir}/dataEPFL/config/config.yaml") - spa = SpecsAnalyzer(config=config_path) + config_path = os.fspath(f"{test_dir}/data/dataEPFL/config/config.yaml") + calib_config = {"calib2d_file": f"{test_dir}/data/phoibos150.calib2d"} + spa = SpecsAnalyzer(config=calib_config, user_config=config_path) calib2d_dict = spa.calib2d lens_mode = "WideAngleMode" kinetic_energy = 35.000000 @@ -75,9 +71,10 @@ def test_conversion_matrix(): """Check the consistency of the conversion matrix with the Igor calculations. """ - igor_data_path = os.fspath(f"{test_dir}/dataEPFL/R9132") - config_path = os.fspath(f"{test_dir}/dataEPFL/config/config.yaml") - spa = SpecsAnalyzer(config=config_path) + igor_data_path = os.fspath(f"{test_dir}/data/dataEPFL/R9132") + config_path = os.fspath(f"{test_dir}/data/dataEPFL/config/config.yaml") + calib_config = {"calib2d_file": f"{test_dir}/data/phoibos150.calib2d"} + spa = SpecsAnalyzer(config=calib_config, user_config=config_path) calib2d_dict = spa.calib2d lens_mode = "WideAngleMode" kinetic_energy = 35.000000 @@ -187,20 +184,21 @@ def test_conversion(): # get the raw data raw_image_name = os.fspath( - f"{test_dir}/dataEPFL/R9132/Data9132_RAWDATA.tsv", + f"{test_dir}/data/dataEPFL/R9132/Data9132_RAWDATA.tsv", ) with open(raw_image_name, encoding="utf-8") as file: tsv_data = np.loadtxt(file, delimiter="\t") # get the reference data reference_image_name = os.fspath( - f"{test_dir}/dataEPFL/R9132/Data9132_IGOR_corrected.tsv", + f"{test_dir}/data/dataEPFL/R9132/Data9132_IGOR_corrected.tsv", ) with open(reference_image_name, encoding="utf-8") as file: reference = np.loadtxt(file, delimiter="\t") - config_path = os.fspath(f"{test_dir}/dataEPFL/config/config.yaml") - spa = SpecsAnalyzer(config=config_path) + config_path = os.fspath(f"{test_dir}/data/dataEPFL/config/config.yaml") + calib_config = {"calib2d_file": f"{test_dir}/data/phoibos150.calib2d"} + spa = SpecsAnalyzer(config=calib_config, user_config=config_path) lens_mode = "WideAngleMode" kinetic_energy = 35.000000 pass_energy = 35.000000 @@ -229,14 +227,14 @@ def test_conversion_from_dict(): # get the raw data raw_image_name = os.fspath( - f"{test_dir}/dataEPFL/R9132/Data9132_RAWDATA.tsv", + f"{test_dir}/data/dataEPFL/R9132/Data9132_RAWDATA.tsv", ) with open(raw_image_name, encoding="utf-8") as file: tsv_data = np.loadtxt(file, delimiter="\t") # get the reference data reference_image_name = os.fspath( - f"{test_dir}/dataEPFL/R9132/Data9132_IGOR_corrected.tsv", + f"{test_dir}/data/dataEPFL/R9132/Data9132_IGOR_corrected.tsv", ) with open(reference_image_name, encoding="utf-8") as file: reference = np.loadtxt(file, delimiter="\t") @@ -309,13 +307,14 @@ def test_recycling(): """ # get the raw data raw_image_name = os.fspath( - f"{test_dir}/dataEPFL/R9132/Data9132_RAWDATA.tsv", + f"{test_dir}/data/dataEPFL/R9132/Data9132_RAWDATA.tsv", ) with open(raw_image_name, encoding="utf-8") as file: tsv_data = np.loadtxt(file, delimiter="\t") - config_path = os.fspath(f"{test_dir}/dataEPFL/config/config.yaml") - spa = SpecsAnalyzer(config=config_path) + config_path = os.fspath(f"{test_dir}/data/dataEPFL/config/config.yaml") + calib_config = {"calib2d_file": f"{test_dir}/data/phoibos150.calib2d"} + spa = SpecsAnalyzer(config=calib_config, user_config=config_path) lens_mode = "WideAngleMode" kinetic_energy = 35.000000 pass_energy = 35.000000 @@ -348,13 +347,14 @@ def test_cropping(): """Test function for checking that cropping parameters are correctly applied""" # get the raw data raw_image_name = os.fspath( - f"{test_dir}/dataEPFL/R9132/Data9132_RAWDATA.tsv", + f"{test_dir}/data/dataEPFL/R9132/Data9132_RAWDATA.tsv", ) with open(raw_image_name, encoding="utf-8") as file: tsv_data = np.loadtxt(file, delimiter="\t") - config_path = os.fspath(f"{test_dir}/dataEPFL/config/config.yaml") - spa = SpecsAnalyzer(config=config_path) + config_path = os.fspath(f"{test_dir}/data/dataEPFL/config/config.yaml") + calib_config = {"calib2d_file": f"{test_dir}/data/phoibos150.calib2d"} + spa = SpecsAnalyzer(config=calib_config, user_config=config_path) lens_mode = "WideAngleMode" kinetic_energy = 35.000000 pass_energy = 35.000000 diff --git a/tests/test_helpers.py b/tests/test_helpers.py index 034b089..e1c9f42 100644 --- a/tests/test_helpers.py +++ b/tests/test_helpers.py @@ -11,11 +11,11 @@ from specsscan.core import load_images from specsscan.core import parse_lut_to_df -package_dir = os.path.dirname(specsscan.__file__) +test_dir = os.path.dirname(__file__) # Path to a sample 3-D scan -scan_path_mirror = Path(f"{package_dir}/../tests/data/4450") +scan_path_mirror = Path(f"{test_dir}/data/4450") # Path to a sample 2-D scan -scan_path_single = Path(f"{package_dir}/../tests/data/3610") +scan_path_single = Path(f"{test_dir}/data/3610") df_lut = parse_lut_to_df(scan_path_mirror) diff --git a/tests/test_lens_modes.py b/tests/test_lens_modes.py index 675b5f2..bda9f2a 100644 --- a/tests/test_lens_modes.py +++ b/tests/test_lens_modes.py @@ -38,8 +38,9 @@ def test_lens_modes_angle(lens_mode): with open(raw_image_name, encoding="utf-8") as file: tsv_data = np.loadtxt(file, delimiter="\t") - configpath = os.fspath(f"{test_dir}/data/dataEPFL/config/config.yaml") - spa = SpecsAnalyzer(config=configpath) + config_path = os.fspath(f"{test_dir}/data/dataEPFL/config/config.yaml") + calib_config = {"calib2d_file": f"{test_dir}/data/phoibos150.calib2d"} + spa = SpecsAnalyzer(config=calib_config, user_config=config_path) kinetic_energy = np.random.uniform(20, 50) pass_energy = np.random.uniform(20, 50) work_function = 4.2 @@ -67,8 +68,9 @@ def test_lens_modes_space(lens_mode): with open(raw_image_name, encoding="utf-8") as file: tsv_data = np.loadtxt(file, delimiter="\t") - configpath = os.fspath(f"{test_dir}/data/dataEPFL/config/config.yaml") - spa = SpecsAnalyzer(config=configpath) + config_path = os.fspath(f"{test_dir}/data/dataEPFL/config/config.yaml") + calib_config = {"calib2d_file": f"{test_dir}/data/phoibos150.calib2d"} + spa = SpecsAnalyzer(config=calib_config, user_config=config_path) kinetic_energy = np.random.uniform(20, 50) pass_energy = np.random.uniform(20, 50) work_function = 4.2 @@ -95,8 +97,9 @@ def test_lens_raise(): with open(raw_image_name, encoding="utf-8") as file: tsv_data = np.loadtxt(file, delimiter="\t") - configpath = os.fspath(f"{test_dir}/data/dataEPFL/config/config.yaml") - spa = SpecsAnalyzer(config=configpath) + config_path = os.fspath(f"{test_dir}/data/dataEPFL/config/config.yaml") + calib_config = {"calib2d_file": f"{test_dir}/data/phoibos150.calib2d"} + spa = SpecsAnalyzer(config=calib_config, user_config=config_path) kinetic_energy = 35.000000 pass_energy = 35.000000 work_function = 4.2 diff --git a/tests/test_specsanalyzer.py b/tests/test_specsanalyzer.py index 9d44b37..b97ddfa 100755 --- a/tests/test_specsanalyzer.py +++ b/tests/test_specsanalyzer.py @@ -1,4 +1,5 @@ """This is a code that performs several tests for the SpecsAnalyzer core class functions""" +import importlib.metadata import os from importlib.util import find_spec @@ -10,7 +11,7 @@ def test_version(): """Test if the package has the correct version string.""" - assert __version__ == "0.1.0" + assert __version__ == importlib.metadata.version("specsanalyzer") def test_default_config(): diff --git a/tests/test_specsscan.py b/tests/test_specsscan.py index dd1b896..1ea674a 100755 --- a/tests/test_specsscan.py +++ b/tests/test_specsscan.py @@ -1,5 +1,6 @@ """This is a code that performs several tests for the SpecsScan core class functions """ +import importlib.metadata import os import numpy as np @@ -12,13 +13,15 @@ from specsscan import SpecsScan package_dir = os.path.dirname(specsscan.__file__) -test_dir = package_dir + "/../tests/data/" +test_dir = package_dir + "/../../tests/data/" +test_dir = os.path.dirname(__file__) +data_dir = os.fspath(f"{test_dir}/data/") fft_filter_peaks = create_fft_params(amplitude=1, pos_x=82, pos_y=116, sigma_x=15, sigma_y=23) def test_version(): """Test if the package has the correct version string.""" - assert __version__ == "0.1.0" + assert __version__ == importlib.metadata.version("specsanalyzer") def test_default_config(): @@ -31,41 +34,27 @@ def test_default_config(): def test_conversion_2d(): """Test the conversion of a single-image scan""" - sps = SpecsScan( - config=test_dir + "config.yaml", - user_config={}, - system_config={}, - ) - res_xarray = sps.load_scan( - scan=3610, - path=test_dir, - ) + config_path = os.fspath(f"{test_dir}/data/config.yaml") + calib_config = {"spa_params": {"calib2d_file": f"{test_dir}/data/phoibos150.calib2d"}} + sps = SpecsScan(config=calib_config, user_config=config_path, system_config={}) + res_xarray = sps.load_scan(scan=3610, path=data_dir) assert res_xarray.dims == ("Angle", "Ekin") with pytest.raises(IndexError): - res_xarray = sps.load_scan( - scan=3610, - path=test_dir, - iterations=[0], - ) + res_xarray = sps.load_scan(scan=3610, path=data_dir, iterations=[0]) def test_conversion_3d(): """Test the conversion of a 3D scan""" - sps = SpecsScan( - config=test_dir + "config.yaml", - user_config={}, - system_config={}, - ) - res_xarray = sps.load_scan( - scan=4450, - path=test_dir, - ) + config_path = os.fspath(f"{test_dir}/data/config.yaml") + calib_config = {"spa_params": {"calib2d_file": f"{test_dir}/data/phoibos150.calib2d"}} + sps = SpecsScan(config=calib_config, user_config=config_path, system_config={}) + res_xarray = sps.load_scan(scan=4450, path=data_dir) assert res_xarray.dims == ("Angle", "Ekin", "mirrorX") res_xarray2 = sps.load_scan( scan=4450, - path=test_dir, + path=data_dir, iterations=[0], ) np.testing.assert_raises( @@ -77,7 +66,7 @@ def test_conversion_3d(): res_xarray2 = sps.load_scan( scan=4450, - path=test_dir, + path=data_dir, iterations=np.s_[0:2], ) np.testing.assert_allclose(res_xarray, res_xarray2) @@ -86,7 +75,7 @@ def test_conversion_3d(): sps.load_scan( scan=4450, iterations=range(1, 20), - path=test_dir, + path=data_dir, ) @@ -100,7 +89,7 @@ def test_conversion_from_convert_dict(): with pytest.raises(ValueError): res_xarray = sps.load_scan( scan=4450, - path=test_dir, + path=data_dir, ) conversion_parameters = { @@ -132,7 +121,7 @@ def test_conversion_from_convert_dict(): res_xarray = sps.load_scan( scan=4450, - path=test_dir, + path=data_dir, conversion_parameters=conversion_parameters, ) @@ -142,16 +131,14 @@ def test_conversion_from_convert_dict(): def test_checkscan(): """Test the check_scan function""" - sps = SpecsScan( - config=test_dir + "config.yaml", - user_config={}, - system_config={}, - ) + config_path = os.fspath(f"{test_dir}/data/config.yaml") + calib_config = {"spa_params": {"calib2d_file": f"{test_dir}/data/phoibos150.calib2d"}} + sps = SpecsScan(config=calib_config, user_config=config_path, system_config={}) res_xarray = sps.check_scan( scan=4450, delays=[0], - path=test_dir, + path=data_dir, ) assert res_xarray.dims == ("Angle", "Ekin", "Iteration") @@ -159,23 +146,21 @@ def test_checkscan(): sps.check_scan( scan=4450, delays=range(1, 20), - path=test_dir, + path=data_dir, ) def test_checkscan_2d_raises(): """Test that the check_scan function raises if a single image is loaded""" - sps = SpecsScan( - config=test_dir + "config.yaml", - user_config={}, - system_config={}, - ) + config_path = os.fspath(f"{test_dir}/data/config.yaml") + calib_config = {"spa_params": {"calib2d_file": f"{test_dir}/data/phoibos150.calib2d"}} + sps = SpecsScan(config=calib_config, user_config=config_path, system_config={}) with pytest.raises(ValueError): sps.check_scan( scan=3610, delays=[0], - path=test_dir, + path=data_dir, ) @@ -183,6 +168,7 @@ def test_process_sweep_scan(): """Test the conversion of a sweep scan""" config = { "spa_params": { + "calib2d_file": f"{test_dir}/data/phoibos150.calib2d", "ek_range_min": 0.07597844332538357, "ek_range_max": 0.8965456312395133, "ang_range_min": 0.16732026143790849, @@ -199,7 +185,7 @@ def test_process_sweep_scan(): ) res_xarray = sps.load_scan( scan=6455, - path=test_dir, + path=data_dir, ) assert res_xarray.energy[0].values.item() == 20.953256232558136 assert res_xarray.energy[-1].values.item() == 21.02424460465116 @@ -210,15 +196,13 @@ def test_process_sweep_scan(): def test_crop_tool(): """Test the crop tool""" - sps = SpecsScan( - config=test_dir + "config.yaml", - user_config={}, - system_config={}, - ) + config_path = os.fspath(f"{test_dir}/data/config.yaml") + calib_config = {"spa_params": {"calib2d_file": f"{test_dir}/data/phoibos150.calib2d"}} + sps = SpecsScan(config=calib_config, user_config=config_path, system_config={}) res_xarray = sps.load_scan( scan=3610, - path=test_dir, + path=data_dir, crop=True, ) @@ -231,7 +215,7 @@ def test_crop_tool(): res_xarray = sps.load_scan( scan=3610, - path=test_dir, + path=data_dir, ek_range_min=0.1, ek_range_max=0.9, ang_range_min=0.1, @@ -255,7 +239,7 @@ def test_crop_tool(): res_xarray = sps.load_scan( scan=3610, - path=test_dir, + path=data_dir, ) assert res_xarray.Angle[0] == -14.34375 assert res_xarray.Angle[-1] == 14.203125 @@ -267,15 +251,12 @@ def test_crop_tool(): def test_fft_tool(): """Test the fft tool""" - - sps = SpecsScan( - config=test_dir + "config.yaml", - user_config={}, - system_config={}, - ) + config_path = os.fspath(f"{test_dir}/data/config.yaml") + calib_config = {"spa_params": {"calib2d_file": f"{test_dir}/data/phoibos150.calib2d"}} + sps = SpecsScan(config=calib_config, user_config=config_path, system_config={}) res_xarray = sps.load_scan( scan=3610, - path=test_dir, + path=data_dir, apply_fft_filter=False, ) @@ -283,7 +264,7 @@ def test_fft_tool(): res_xarray = sps.load_scan( scan=3610, - path=test_dir, + path=data_dir, fft_filter_peaks=fft_filter_peaks, apply_fft_filter=True, ) @@ -299,13 +280,16 @@ def test_fft_tool(): ) assert sps.config["spa_params"]["fft_filter_peaks"] == fft_filter_peaks assert sps.spa.config["fft_filter_peaks"] == fft_filter_peaks - res_xarray = sps.load_scan(scan=3610, path=test_dir, apply_fft_filter=True) + res_xarray = sps.load_scan(scan=3610, path=data_dir, apply_fft_filter=True) np.testing.assert_almost_equal(res_xarray.data.sum(), 62197237155.50347, decimal=3) def test_conversion_and_save_to_nexus(): """Test the conversion of a tilt scan and saving as NeXus""" - config = {"nexus": {"input_files": [package_dir + "/config/NXmpes_arpes_config.json"]}} + config = { + "nexus": {"input_files": [package_dir + "/config/NXmpes_arpes_config.json"]}, + "spa_params": {"calib2d_file": f"{test_dir}/data/phoibos150.calib2d"}, + } sps = SpecsScan( config=config, user_config=package_dir + "/config/example_config_FHI.yaml", @@ -314,7 +298,7 @@ def test_conversion_and_save_to_nexus(): res_xarray = sps.load_scan( scan=1496, - path=test_dir, + path=data_dir, crop=True, ) @@ -356,7 +340,7 @@ def test_conversion_and_save_to_nexus(): metadata["scan_info"]["trARPES:Sample:Measure"] = 0 res_xarray = sps.load_scan( scan=1496, - path=test_dir, + path=data_dir, crop=True, metadata=metadata, collect_metadata=True, diff --git a/tutorial/3_specsscan_conversion_to_NeXus.ipynb b/tutorial/3_specsscan_conversion_to_NeXus.ipynb index 859db31..22d19fd 100755 --- a/tutorial/3_specsscan_conversion_to_NeXus.ipynb +++ b/tutorial/3_specsscan_conversion_to_NeXus.ipynb @@ -125,7 +125,7 @@ "outputs": [], "source": [ "config = {\"nexus\":{\"definition\": \"NXmpes_arpes\"}, \"spa_params\":{\"crop\":True, \"ek_range_min\":0.07597844332538181, \"ek_range_max\":0.9117413199045858, \"ang_range_min\":0.16453159041394336, \"ang_range_max\":0.8840087145969499,}}\n", - "sps = SpecsScan(config=config, user_config=\"../specsscan/config/example_config_FHI.yaml\")\n", + "sps = SpecsScan(config=config, user_config=\"../src/specsscan/config/example_config_FHI.yaml\")\n", "path = \"../tests/data/\" # Path to the test data set" ] }, diff --git a/tutorial/4_specsscan_load_sweep_scan.ipynb b/tutorial/4_specsscan_load_sweep_scan.ipynb index 1d58e58..a7c078a 100644 --- a/tutorial/4_specsscan_load_sweep_scan.ipynb +++ b/tutorial/4_specsscan_load_sweep_scan.ipynb @@ -48,7 +48,7 @@ " \"rotation_angle\": 2,\n", " \"crop\":True,\n", "}}\n", - "sps = SpecsScan(config=config, user_config=\"../specsscan/config/example_config_FHI.yaml\")\n", + "sps = SpecsScan(config=config, user_config=\"../src/specsscan/config/example_config_FHI.yaml\")\n", "path = \"../tests/data/\" # Path to the test data set" ] },