From 883c38482c9a9e319c2ac2e253af279de1f8c4bf Mon Sep 17 00:00:00 2001 From: Andrew Sazonov Date: Fri, 19 Dec 2025 21:11:21 +0100 Subject: [PATCH 1/2] Fixes backmerge workflow app token inputs --- .github/workflows/backmerge-pr.yaml | 10 ++++++---- 1 file changed, 6 insertions(+), 4 deletions(-) diff --git a/.github/workflows/backmerge-pr.yaml b/.github/workflows/backmerge-pr.yaml index 8cfe84ae..44d1189d 100644 --- a/.github/workflows/backmerge-pr.yaml +++ b/.github/workflows/backmerge-pr.yaml @@ -7,6 +7,8 @@ # The GitHub App must be added to the develop ruleset bypass list. # # Required repo config: +# https://github.com/organizations/easyscience/settings/secrets/actions +# https://github.com/organizations/easyscience/settings/variables/actions # - Actions secret: ES_BACKMERGE_PRIVATE_KEY (GitHub App private key PEM) # - Actions variable: ES_BACKMERGE_APP_ID (GitHub App ID) @@ -14,8 +16,8 @@ name: Backmerge PR (tag -> develop) on: push: - tags: - - 'v*' + branches: ['**'] + tags: ['v*'] permissions: contents: write @@ -30,8 +32,8 @@ jobs: id: app-token uses: actions/create-github-app-token@v2 with: - app-id: ${{ secrets.ES_BACKMERGE_APP_ID }} # in secrets or vars? - private-key: ${{ secrets.ES_BACKMERGE_PRIVATE_KEY }} + app-id: ${{ vars.BACKMERGE_APP_ID }} + private-key: ${{ secrets.BACKMERGE_PRIVATE_KEY }} - name: Checkout tag commit uses: actions/checkout@v5 From 64bd29fe5b8786cf8096038d6d387f0c0cc954ca Mon Sep 17 00:00:00 2001 From: Andrew Sazonov Date: Wed, 24 Dec 2025 22:13:01 +0100 Subject: [PATCH 2/2] Expose tutorials via gh-pages with listing and selective download API (#112) * Restricts backmerge workflow to release tags * Updates release PR workflow name * Unifies docs deployment URL handling * Promotes Step 5 heading to H2 in tutorial * Fetches full history for docs deployment * Disables notebook run to speed docs build * Standardizes tutorial IDs to ed-*; updates nav * Adds tutorials index JSON with versioned links * Adds per-tutorial downloads via gh-pages index * Expands docs task to move all tutorial files * Removes tutorial packaging from release workflow * Adds PYTHONPATH and version diagnostics in CI * Replaces pixi add with uv pip install in CI * Pins numpy * Update deps * Re-enables notebook execution in docs CI * Uses pixi add for wheel install in CI * Pin bootstrap pip install to release version * Replaces pixi add with uv pip for wheel install --- .github/workflows/backmerge-pr.yaml | 3 +- .github/workflows/docs.yaml | 22 +- .github/workflows/release-notes.yaml | 11 - .github/workflows/release-pr.yaml | 2 +- .github/workflows/test.yaml | 8 +- docs/mkdocs.yml | 26 +- docs/tutorials/index.md | 105 +- docs/user-guide/first-steps.md | 4 +- pixi.lock | 2112 +++++++++-------- pixi.toml | 2 +- pyproject.toml | 1 + src/easydiffraction/__init__.py | 6 +- src/easydiffraction/__main__.py | 41 +- src/easydiffraction/utils/__init__.py | 8 + src/easydiffraction/utils/utils.py | 345 +-- tests/unit/easydiffraction/test___init__.py | 12 +- tests/unit/easydiffraction/test___main__.py | 20 +- .../unit/easydiffraction/utils/test_utils.py | 220 +- tools/tweak_notebooks.py | 69 +- ...m-cif_pd-neut-cwl_LBCO-HRPT.py => ed-1.py} | 2 +- tutorials/{pdf_pd-neut-cwl_Ni.py => ed-10.py} | 0 .../{pdf_pd-neut-tof_Si-NOMAD.py => ed-11.py} | 0 tutorials/{pdf_pd-xray_NaCl.py => ed-12.py} | 0 ...nalysis-powder-diffraction.py => ed-13.py} | 0 ...-code_pd-neut-cwl_LBCO-HRPT.py => ed-2.py} | 0 ...e-fit_pd-neut-cwl_LBCO-HRPT.py => ed-3.py} | 0 ...-fit_pd-neut-xray-cwl_PbSO4.py => ed-4.py} | 0 ...ruct_pd-neut-cwl_CoSiO4-D20.py => ed-5.py} | 0 ...-struct_pd-neut-cwl_HS-HRPT.py => ed-6.py} | 0 ...-struct_pd-neut-tof_Si-SEPD.py => ed-7.py} | 0 ...eut-tof_multidata_NCAF-WISH.py => ed-8.py} | 0 ...f_multiphase-LBCO-Si_McStas.py => ed-9.py} | 0 tutorials/index.json | 93 + 33 files changed, 1827 insertions(+), 1285 deletions(-) rename tutorials/{quick_from-cif_pd-neut-cwl_LBCO-HRPT.py => ed-1.py} (98%) rename tutorials/{pdf_pd-neut-cwl_Ni.py => ed-10.py} (100%) rename tutorials/{pdf_pd-neut-tof_Si-NOMAD.py => ed-11.py} (100%) rename tutorials/{pdf_pd-xray_NaCl.py => ed-12.py} (100%) rename tutorials/{dmsc-summer-school-2025_analysis-powder-diffraction.py => ed-13.py} (100%) rename tutorials/{quick_from-code_pd-neut-cwl_LBCO-HRPT.py => ed-2.py} (100%) rename tutorials/{basic_single-fit_pd-neut-cwl_LBCO-HRPT.py => ed-3.py} (100%) rename tutorials/{advanced_joint-fit_pd-neut-xray-cwl_PbSO4.py => ed-4.py} (100%) rename tutorials/{cryst-struct_pd-neut-cwl_CoSiO4-D20.py => ed-5.py} (100%) rename tutorials/{cryst-struct_pd-neut-cwl_HS-HRPT.py => ed-6.py} (100%) rename tutorials/{cryst-struct_pd-neut-tof_Si-SEPD.py => ed-7.py} (100%) rename tutorials/{cryst-struct_pd-neut-tof_multidata_NCAF-WISH.py => ed-8.py} (100%) rename tutorials/{cryst-struct_pd-neut-tof_multiphase-LBCO-Si_McStas.py => ed-9.py} (100%) create mode 100644 tutorials/index.json diff --git a/.github/workflows/backmerge-pr.yaml b/.github/workflows/backmerge-pr.yaml index 44d1189d..f21a5a30 100644 --- a/.github/workflows/backmerge-pr.yaml +++ b/.github/workflows/backmerge-pr.yaml @@ -16,7 +16,6 @@ name: Backmerge PR (tag -> develop) on: push: - branches: ['**'] tags: ['v*'] permissions: @@ -73,7 +72,7 @@ jobs: BODY="⚠️ This PR is created automatically for backmerge of a new release tag commit \`${{ steps.vars.outputs.tag }}\` into \`develop\`. - It is labeled '[maintainer] auto-pull-request' and is excluded from release notes and version bump logic." + It is labeled `[maintainer] auto-pull-request` and is excluded from release notes and version bump logic." if gh pr view --repo "${{ github.repository }}" --head "${{ steps.vars.outputs.branch }}" >/dev/null 2>&1; then echo "PR already exists for head=${{ steps.vars.outputs.branch }}" diff --git a/.github/workflows/docs.yaml b/.github/workflows/docs.yaml index 23e54ff1..46542289 100644 --- a/.github/workflows/docs.yaml +++ b/.github/workflows/docs.yaml @@ -51,9 +51,6 @@ env: IS_RELEASE_TAG: ${{ startsWith(github.ref, 'refs/tags/v') }} GITHUB_REPOSITORY: ${{ github.repository }} NOTEBOOKS_DIR: tutorials - DEV_DEPLOYMENT_URL: - https://easyscience.github.io/${{ github.event.repository.name }}/dev - PROD_DEPLOYMENT_URL: https://docs.easydiffraction.org/lib jobs: # Job 1: Build the static files for the documentation site @@ -72,6 +69,10 @@ jobs: # main.html template. It defines the versioned docs subfolder name # in the gh-pages branch. If it's a release tag, use the version # number without the 'v' prefix, otherwise use 'dev'. + # Setting RELEASE_VERSION to be used in mkdocs.yml to show + # the latest release version in the index.md file. If it's a + # release tag, use the tag name, otherwise use the branch name + # for development builds. - name: Set extra env variables shell: bash run: | @@ -84,19 +85,12 @@ jobs: fi echo "RELEASE_VERSION=${RELEASE_VERSION}" >> "$GITHUB_ENV" echo "DOCS_VERSION=${DOCS_VERSION}" >> "$GITHUB_ENV" + echo "DEPLOYMENT_URL=https://easyscience.github.io/${{ github.event.repository.name }}/${DOCS_VERSION}" >> "$GITHUB_ENV" - name: Check-out repository uses: actions/checkout@v5 with: - fetch-depth: 0 # full history + tags. needed to get the latest release version - - # Save the latest release version of easyscience/diffraction-lib to RELEASE_VERSION - # RELEASE_VERSION is used in the mkdocs.yml file to set release_version. - # The release_version is then needed to display the latest release version in the index.md file - #- name: Set RELEASE_VERSION env variable (latest easydiffraction release) - # run: | - # git fetch --tags --force - # echo "RELEASE_VERSION=$(git describe --tags --abbrev=0)" >> "$GITHUB_ENV" + fetch-depth: 0 # full history with tags; needed for mike to push/deploy docs # Activate dark mode to create documentation with Plotly charts in dark mode # Need a better solution to automatically switch the chart colour theme based on the mkdocs material switcher @@ -147,6 +141,7 @@ jobs: # Run the notebooks to generate the output cells using multiple cores - name: Run notebooks + # if: false # Temporarily disabled to speed up the docs build run: pixi run notebook-exec - name: Move notebooks to docs/tutorials @@ -190,9 +185,8 @@ jobs: run: | if [[ "${IS_RELEASE_TAG}" == "true" ]]; then pixi run docs-deploy "${RELEASE_VERSION#v}" latest - echo "πŸ”— PROD deployment url [${{ env.PROD_DEPLOYMENT_URL }}](${{ env.PROD_DEPLOYMENT_URL }})" >> $GITHUB_STEP_SUMMARY else pixi run docs-deploy dev - echo "πŸ”— DEV deployment url [${{ env.DEV_DEPLOYMENT_URL }}](${{ env.DEV_DEPLOYMENT_URL }})" >> $GITHUB_STEP_SUMMARY fi pixi run docs-set-default latest + echo "πŸ”— deployment url [${{ env.DEPLOYMENT_URL }}](${{ env.DEPLOYMENT_URL }})" >> $GITHUB_STEP_SUMMARY diff --git a/.github/workflows/release-notes.yaml b/.github/workflows/release-notes.yaml index 369449da..f92c7c34 100644 --- a/.github/workflows/release-notes.yaml +++ b/.github/workflows/release-notes.yaml @@ -38,15 +38,6 @@ jobs: shell: bash run: pixi run dev - - name: Convert tutorial scripts to notebooks - run: pixi run notebook-prepare - - - name: Clean up unnecessary script files - run: rm -rf tutorials/*.py - - - name: Zip the tutorials directory - run: zip -9 -r tutorials.zip tutorials - - name: Drafts the next release notes id: draft uses: enhantica/drafterino@v2 @@ -81,7 +72,5 @@ jobs: tag_name: ${{ steps.draft.outputs.tag_name }} name: ${{ steps.draft.outputs.release_name }} body: ${{ steps.draft.outputs.release_notes }} - files: | - tutorials.zip env: GITHUB_TOKEN: ${{ secrets.GITHUB_TOKEN }} diff --git a/.github/workflows/release-pr.yaml b/.github/workflows/release-pr.yaml index 7c45c41c..8f028fd6 100644 --- a/.github/workflows/release-pr.yaml +++ b/.github/workflows/release-pr.yaml @@ -6,7 +6,7 @@ # - Adds the label "[maintainer] auto-pull-request" so it is excluded from changelogs. # - The PR body makes clear that this is automation only (no review needed). -name: Release PR creation +name: Release PR (develop -> master) on: # Allows you to run this workflow manually from the Actions tab diff --git a/.github/workflows/test.yaml b/.github/workflows/test.yaml index 4d57a22a..13945fbf 100644 --- a/.github/workflows/test.yaml +++ b/.github/workflows/test.yaml @@ -206,16 +206,16 @@ jobs: pixi run --environment $env wheel done - - name: Add easydiffraction package from the built wheel + - name: Install easydiffraction package from the built wheel shell: bash run: | for env in ${{ env.PIXI_ENVS }}; do echo "πŸ”ΉπŸ”ΈπŸ”ΉπŸ”ΈπŸ”Ή Current env: $env πŸ”ΉπŸ”ΈπŸ”ΉπŸ”ΈπŸ”Ή" env_prefix="${env%%-*}" echo "πŸ“¦ Looking for wheel in dist/$env_prefix/" - whl_path="$(python3 -c "import pathlib; w = sorted(pathlib.Path('dist/${env_prefix}').glob('*.whl')); print(w[0].resolve().as_uri())")" - echo "πŸ“¦ Adding easydiffraction from: $whl_path" - pixi add --feature $env_prefix --pypi "easydiffraction[all] @ $whl_path" + whl_path="$(find dist/${env_prefix} -name '*.whl' | head -1)" + echo "πŸ“¦ Installing easydiffraction from: $whl_path" + pixi run --environment $env python -m uv pip install "${whl_path}[all]" --reinstall-package easydiffraction pixi run --environment $env easydiffraction --version done diff --git a/docs/mkdocs.yml b/docs/mkdocs.yml index aea235ff..6641a35b 100644 --- a/docs/mkdocs.yml +++ b/docs/mkdocs.yml @@ -69,22 +69,22 @@ nav: - Tutorials: - Tutorials: tutorials/index.md - Getting Started: - - LBCO quick CIF: tutorials/quick_from-cif_pd-neut-cwl_LBCO-HRPT.ipynb - - LBCO quick code: tutorials/quick_from-code_pd-neut-cwl_LBCO-HRPT.ipynb - - LBCO basic: tutorials/basic_single-fit_pd-neut-cwl_LBCO-HRPT.ipynb - - PbSO4 advanced: tutorials/advanced_joint-fit_pd-neut-xray-cwl_PbSO4.ipynb + - LBCO quick CIF: tutorials/ed-1.ipynb + - LBCO quick code: tutorials/ed-2.ipynb + - LBCO basic: tutorials/ed-3.ipynb + - PbSO4 advanced: tutorials/ed-4.ipynb - Standard Diffraction: - - Co2SiO4 pd-neut-cwl: tutorials/cryst-struct_pd-neut-cwl_CoSiO4-D20.ipynb - - HS pd-neut-cwl: tutorials/cryst-struct_pd-neut-cwl_HS-HRPT.ipynb - - Si pd-neut-tof: tutorials/cryst-struct_pd-neut-tof_Si-SEPD.ipynb - - NCAF pd-neut-tof: tutorials/cryst-struct_pd-neut-tof_multidata_NCAF-WISH.ipynb - - LBCO+Si McStas: tutorials/cryst-struct_pd-neut-tof_multiphase-LBCO-Si_McStas.ipynb + - Co2SiO4 pd-neut-cwl: tutorials/ed-5.ipynb + - HS pd-neut-cwl: tutorials/ed-6.ipynb + - Si pd-neut-tof: tutorials/ed-7.ipynb + - NCAF pd-neut-tof: tutorials/ed-8.ipynb + - LBCO+Si McStas: tutorials/ed-9.ipynb - Pair Distribution Function: - - Ni pd-neut-cwl: tutorials/pdf_pd-neut-cwl_Ni.ipynb - - Si pd-neut-tof: tutorials/pdf_pd-neut-tof_Si-NOMAD.ipynb - - NaCl pd-xray: tutorials/pdf_pd-xray_NaCl.ipynb + - Ni pd-neut-cwl: tutorials/ed-10.ipynb + - Si pd-neut-tof: tutorials/ed-11.ipynb + - NaCl pd-xray: tutorials/ed-12.ipynb - Workshops & Schools: - - 2025 DMSC: tutorials/dmsc-summer-school-2025_analysis-powder-diffraction.ipynb + - 2025 DMSC: tutorials/ed-13.ipynb - API Reference: - API Reference: api-reference/index.md - analysis: api-reference/analysis.md diff --git a/docs/tutorials/index.md b/docs/tutorials/index.md index 5ce91a38..55f406a4 100644 --- a/docs/tutorials/index.md +++ b/docs/tutorials/index.md @@ -17,68 +17,63 @@ The tutorials are organized into the following categories. ## Getting Started -- [LBCO `quick` CIF](quick_from-cif_pd-neut-cwl_LBCO-HRPT.ipynb) – A minimal - example intended as a quick reference for users already familiar with the - EasyDiffraction API or who want to see how Rietveld refinement of the - La0.5Ba0.5CoO3 crystal structure can be performed when both the sample model - and experiment are loaded from CIF files. Data collected from constant - wavelength neutron powder diffraction at HRPT at PSI. -- [LBCO `quick` `code`](quick_from-code_pd-neut-cwl_LBCO-HRPT.ipynb) – A minimal - example intended as a quick reference for users already familiar with the - EasyDiffraction API or who want to see an example refinement when both the - sample model and experiment are defined directly in code. This tutorial covers - a Rietveld refinement of the La0.5Ba0.5CoO3 crystal structure using constant - wavelength neutron powder diffraction data from HRPT at PSI. -- [LBCO `basic`](basic_single-fit_pd-neut-cwl_LBCO-HRPT.ipynb) – Demonstrates - the use of the EasyDiffraction API in a simplified, user-friendly manner that - closely follows the GUI workflow for a Rietveld refinement of the +- [LBCO `quick` CIF](ed-1.ipynb) – A minimal example intended as a quick + reference for users already familiar with the EasyDiffraction API or who want + to see how Rietveld refinement of the La0.5Ba0.5CoO3 crystal structure can be + performed when both the sample model and experiment are loaded from CIF files. + Data collected from constant wavelength neutron powder diffraction at HRPT at + PSI. +- [LBCO `quick` `code`](ed-2.ipynb) – A minimal example intended as a quick + reference for users already familiar with the EasyDiffraction API or who want + to see an example refinement when both the sample model and experiment are + defined directly in code. This tutorial covers a Rietveld refinement of the La0.5Ba0.5CoO3 crystal structure using constant wavelength neutron powder - diffraction data from HRPT at PSI. This tutorial provides a full explanation - of the workflow with detailed comments and descriptions of every step, making - it suitable for users who are new to EasyDiffraction or those who prefer a - more guided approach. -- [PbSO4 `advanced`](advanced_joint-fit_pd-neut-xray-cwl_PbSO4.ipynb) – - Demonstrates a more flexible and advanced approach to using the - EasyDiffraction library, intended for users who are more comfortable with - Python programming. This tutorial covers a Rietveld refinement of the PbSO4 - crystal structure based on the joint fit of both X-ray and neutron diffraction - data. + diffraction data from HRPT at PSI. +- [LBCO `basic`](ed-3.ipynb) – Demonstrates the use of the EasyDiffraction API + in a simplified, user-friendly manner that closely follows the GUI workflow + for a Rietveld refinement of the La0.5Ba0.5CoO3 crystal structure using + constant wavelength neutron powder diffraction data from HRPT at PSI. This + tutorial provides a full explanation of the workflow with detailed comments + and descriptions of every step, making it suitable for users who are new to + EasyDiffraction or those who prefer a more guided approach. +- [PbSO4 `advanced`](ed-4.ipynb) – Demonstrates a more flexible and advanced + approach to using the EasyDiffraction library, intended for users who are more + comfortable with Python programming. This tutorial covers a Rietveld + refinement of the PbSO4 crystal structure based on the joint fit of both X-ray + and neutron diffraction data. ## Standard Diffraction -- [Co2SiO4 `pd-neut-cwl`](cryst-struct_pd-neut-cwl_HS-HRPT.ipynb) – Demonstrates - a Rietveld refinement of the Co2SiO4 crystal structure using constant - wavelength neutron powder diffraction data from D20 at ILL. -- [HS `pd-neut-cwl`](cryst-struct_pd-neut-cwl_HS-HRPT.ipynb) – Demonstrates a - Rietveld refinement of the HS crystal structure using constant wavelength - neutron powder diffraction data from HRPT at PSI. -- [Si `pd-neut-tof`](cryst-struct_pd-neut-tof_Si-SEPD.ipynb) – Demonstrates a - Rietveld refinement of the Si crystal structure using time-of-flight neutron - powder diffraction data from SEPD at Argonne. -- [NCAF `pd-neut-tof`](cryst-struct_pd-neut-tof_multidata_NCAF-WISH.ipynb) – - Demonstrates a Rietveld refinement of the Na2Ca3Al2F14 crystal structure using - two time-of-flight neutron powder diffraction datasets (from two detector - banks) of the WISH instrument at ISIS. -- [LBCO+Si McStas](cryst-struct_pd-neut-tof_multiphase-LBCO-Si_McStas.ipynb) – - Demonstrates a Rietveld refinement of the La0.5Ba0.5CoO3 crystal structure - with a small amount of Si impurity as a secondary phase using time-of-flight - neutron powder diffraction data simulated with McStas. +- [Co2SiO4 `pd-neut-cwl`](ed-5.ipynb) – Demonstrates a Rietveld refinement of + the Co2SiO4 crystal structure using constant wavelength neutron powder + diffraction data from D20 at ILL. +- [HS `pd-neut-cwl`](ed-6.ipynb) – Demonstrates a Rietveld refinement of the HS + crystal structure using constant wavelength neutron powder diffraction data + from HRPT at PSI. +- [Si `pd-neut-tof`](ed-7.ipynb) – Demonstrates a Rietveld refinement of the Si + crystal structure using time-of-flight neutron powder diffraction data from + SEPD at Argonne. +- [NCAF `pd-neut-tof`](ed-8.ipynb) – Demonstrates a Rietveld refinement of the + Na2Ca3Al2F14 crystal structure using two time-of-flight neutron powder + diffraction datasets (from two detector banks) of the WISH instrument at ISIS. +- [LBCO+Si McStas](ed-9.ipynb) – Demonstrates a Rietveld refinement of the + La0.5Ba0.5CoO3 crystal structure with a small amount of Si impurity as a + secondary phase using time-of-flight neutron powder diffraction data simulated + with McStas. ## Pair Distribution Function (PDF) -- [Ni `pd-neut-cwl`](pdf_pd-neut-cwl_Ni.ipynb) – Demonstrates a PDF analysis of - Ni using data collected from a constant wavelength neutron powder diffraction - experiment. -- [Si `pd-neut-tof`](pdf_pd-neut-tof_Si-NOMAD.ipynb) – Demonstrates a PDF - analysis of Si using data collected from a time-of-flight neutron powder - diffraction experiment at NOMAD at SNS. -- [NaCl `pd-xray`](pdf_pd-xray_NaCl.ipynb) – Demonstrates a PDF analysis of NaCl - using data collected from an X-ray powder diffraction experiment. +- [Ni `pd-neut-cwl`](ed-10.ipynb) – Demonstrates a PDF analysis of Ni using data + collected from a constant wavelength neutron powder diffraction experiment. +- [Si `pd-neut-tof`](ed-11.ipynb) – Demonstrates a PDF analysis of Si using data + collected from a time-of-flight neutron powder diffraction experiment at NOMAD + at SNS. +- [NaCl `pd-xray`](ed-12.ipynb) – Demonstrates a PDF analysis of NaCl using data + collected from an X-ray powder diffraction experiment. ## Workshops & Schools -- [2025 DMSC](dmsc-summer-school-2025_analysis-powder-diffraction.ipynb) – A - workshop tutorial that demonstrates a Rietveld refinement of the - La0.5Ba0.5CoO3 crystal structure using time-of-flight neutron powder - diffraction data simulated with McStas. This tutorial is designed for the ESS - DMSC Summer School 2025. +- [2025 DMSC](ed-13.ipynb) – A workshop tutorial that demonstrates a Rietveld + refinement of the La0.5Ba0.5CoO3 crystal structure using time-of-flight + neutron powder diffraction data simulated with McStas. This tutorial is + designed for the ESS DMSC Summer School 2025. diff --git a/docs/user-guide/first-steps.md b/docs/user-guide/first-steps.md index de25f102..0500b189 100644 --- a/docs/user-guide/first-steps.md +++ b/docs/user-guide/first-steps.md @@ -32,7 +32,7 @@ project = ed.Project() ``` A complete tutorial using the `import` syntax can be found -[here](../../tutorials/basic_single-fit_pd-neut-cwl_LBCO-HRPT/). +[here](../../tutorials/ed-3/). ### Importing specific parts @@ -59,7 +59,7 @@ project = Project() ``` A complete tutorial using the `from` syntax can be found -[here](../../tutorials/advanced_joint-fit_pd-neut-xray-cwl_PbSO4/). +[here](../../tutorials/ed-4/). ## Utility functions diff --git a/pixi.lock b/pixi.lock index 152ea96e..0dbf0594 100644 --- a/pixi.lock +++ b/pixi.lock @@ -14,12 +14,13 @@ environments: - conda: https://conda.anaconda.org/conda-forge/noarch/ca-certificates-2025.11.12-hbd8a1cb_0.conda - conda: https://conda.anaconda.org/conda-forge/linux-64/gsl-2.8-hbf7d49c_1.conda - 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conda: https://conda.anaconda.org/conda-forge/linux-64/zstd-1.5.7-hb78ec9c_6.conda sha256: 68f0206ca6e98fea941e5717cec780ed2873ffabc0e1ed34428c061e2c6268c7 md5: 4a13eeac0b5c8e5b8ab496e6c4ddd829 diff --git a/pixi.toml b/pixi.toml index 2fd51c72..ac84b6ee 100644 --- a/pixi.toml +++ b/pixi.toml @@ -174,7 +174,7 @@ notebook-prepare = { depends-on = [ ## πŸ“š Documentation Tasks docs-assets = 'tools/add_assets_to_docs.sh' -docs-notebooks = 'mv tutorials/*.ipynb docs/tutorials/' +docs-notebooks = 'mv tutorials/*.* docs/tutorials/' # *.py, *.ipynb, index.json docs-config = 'python tools/create_mkdocs_yml.py' docs-deploy = 'mike deploy --push --branch gh-pages --update-aliases --alias-type redirect' docs-set-default = 'mike set-default --push --branch gh-pages' diff --git a/pyproject.toml b/pyproject.toml index 5a3f864e..e06bfda1 100644 --- a/pyproject.toml +++ b/pyproject.toml @@ -22,6 +22,7 @@ classifiers = [ ] requires-python = '>=3.11,<3.14' dependencies = [ + 'numpy<2.4', # Numerical computing library; <2.4 required for cryspy 0.9.x compatibility 'colorama', # Color terminal output 'tabulate', # Pretty-print tabular data for terminal output 'asciichartpy', # ASCII charts for terminal output diff --git a/src/easydiffraction/__init__.py b/src/easydiffraction/__init__.py index f7af7a03..2e4e54f5 100644 --- a/src/easydiffraction/__init__.py +++ b/src/easydiffraction/__init__.py @@ -7,8 +7,9 @@ from easydiffraction.utils.logging import Logger from easydiffraction.utils.logging import console from easydiffraction.utils.logging import log +from easydiffraction.utils.utils import download_all_tutorials from easydiffraction.utils.utils import download_data -from easydiffraction.utils.utils import fetch_tutorials +from easydiffraction.utils.utils import download_tutorial from easydiffraction.utils.utils import get_value_from_xye_header from easydiffraction.utils.utils import list_tutorials from easydiffraction.utils.utils import show_version @@ -18,7 +19,8 @@ 'ExperimentFactory', 'SampleModelFactory', 'download_data', - 'fetch_tutorials', + 'download_tutorial', + 'download_all_tutorials', 'list_tutorials', 'get_value_from_xye_header', 'show_version', diff --git a/src/easydiffraction/__main__.py b/src/easydiffraction/__main__.py index b8a63807..e4e79178 100644 --- a/src/easydiffraction/__main__.py +++ b/src/easydiffraction/__main__.py @@ -43,10 +43,43 @@ def list_tutorials(): ed.list_tutorials() -@app.command('fetch-tutorials') -def fetch_tutorials(): - """Download and extract tutorial notebooks.""" - ed.fetch_tutorials() +@app.command('download-tutorial') +def download_tutorial( + id: int = typer.Argument(..., help='Tutorial ID to download.'), + destination: str = typer.Option( + 'tutorials', + '--destination', + '-d', + help='Directory to save the tutorial into.', + ), + overwrite: bool = typer.Option( + False, # noqa: FBT003 - boolean option is intended + '--overwrite', + '-o', + help='Overwrite existing file if present.', + ), +): + """Download a specific tutorial notebook by ID.""" + ed.download_tutorial(id=id, destination=destination, overwrite=overwrite) + + +@app.command('download-all-tutorials') +def download_all_tutorials( + destination: str = typer.Option( + 'tutorials', + '--destination', + '-d', + help='Directory to save the tutorials into.', + ), + overwrite: bool = typer.Option( + False, # noqa: FBT003 - boolean option is intended + '--overwrite', + '-o', + help='Overwrite existing files if present.', + ), +): + """Download all available tutorial notebooks.""" + ed.download_all_tutorials(destination=destination, overwrite=overwrite) if __name__ == '__main__': diff --git a/src/easydiffraction/utils/__init__.py b/src/easydiffraction/utils/__init__.py index 3e95b5e9..4122cfb2 100644 --- a/src/easydiffraction/utils/__init__.py +++ b/src/easydiffraction/utils/__init__.py @@ -1,2 +1,10 @@ # SPDX-FileCopyrightText: 2021-2025 EasyDiffraction contributors # SPDX-License-Identifier: BSD-3-Clause + +from easydiffraction.utils.utils import _is_dev_version +from easydiffraction.utils.utils import stripped_package_version + +__all__ = [ + '_is_dev_version', + 'stripped_package_version', +] diff --git a/src/easydiffraction/utils/utils.py b/src/easydiffraction/utils/utils.py index 4f92a68a..5c07da92 100644 --- a/src/easydiffraction/utils/utils.py +++ b/src/easydiffraction/utils/utils.py @@ -3,13 +3,10 @@ from __future__ import annotations -import io import json -import os import pathlib import re import urllib.request -import zipfile from functools import lru_cache from importlib.metadata import PackageNotFoundError from importlib.metadata import version @@ -94,6 +91,36 @@ def _fetch_data_index() -> dict: return json.load(f) +@lru_cache(maxsize=1) +def _fetch_tutorials_index() -> dict: + """Fetch & cache the tutorials index.json from gh-pages and return + it as dict. + + The index is fetched from: + https://easyscience.github.io/diffraction-lib/{version}/tutorials/index.json + + For released versions, {version} is the public version string + (e.g., '0.8.0.post1'). For development versions, 'dev' is used. + + Returns: + dict: The tutorials index as a dictionary, or empty dict if + fetch fails. + """ + version = _get_version_for_url() + index_url = f'https://easyscience.github.io/diffraction-lib/{version}/tutorials/index.json' + + try: + _validate_url(index_url) + with _safe_urlopen(index_url) as response: + return json.load(response) + except Exception as e: + log.warning( + f'Failed to fetch tutorials index from {index_url}: {e}', + exc_type=UserWarning, + ) + return {} + + def download_data( id: int | str, destination: str = 'data', @@ -208,70 +235,53 @@ def stripped_package_version(package_name: str) -> str | None: return v_str -def _get_release_info(tag: str | None) -> dict | None: - """Fetch release info from GitHub for the given tag (or latest if - None). Uses unauthenticated API by default, but includes - GITHUB_TOKEN from the environment if available to avoid rate - limiting. +def _is_dev_version(package_name: str) -> bool: + """Check if the installed package version is a development/local + version. + + A version is considered "dev" if: + - The raw version contains '+dev', '+dirty', or '+devdirty' (local + suffixes from versioningit) + - The public version is '999.0.0' (versioningit default-tag + fallback) Args: - tag (str | None): The tag of the release to fetch, or None for - latest. + package_name (str): The name of the package to query. Returns: - dict | None: The release info dictionary if retrievable, None - otherwise. + bool: True if the version is a development version, False + otherwise. """ - if tag is not None: - api_url = f'https://api.github.com/repos/easyscience/diffraction-lib/releases/tags/{tag}' - else: - api_url = 'https://api.github.com/repos/easyscience/diffraction-lib/releases/latest' - try: - _validate_url(api_url) - headers = {} - token = os.environ.get('GITHUB_TOKEN') - if token: - headers['Authorization'] = f'token {token}' - request = urllib.request.Request(api_url, headers=headers) # noqa: S310 - constructing request (validated URL) - # Safe network call: HTTPS enforced and validated - with _safe_urlopen(request) as response: - return json.load(response) - except Exception as e: - if tag is not None: - log.error(f'Failed to fetch release info for tag {tag}: {e}') - else: - log.error(f'Failed to fetch latest release info: {e}') - return None - + raw_version = package_version(package_name) + if raw_version is None: + return True # No version found, assume dev -def _get_tutorial_asset(release_info: dict) -> dict | None: - """Given a release_info dict, return the 'tutorials.zip' asset dict, - or None. + # Check for local version suffixes from versioningit + if any(marker in raw_version for marker in ('+dev', '+dirty', '+devdirty')): + return True - Args: - release_info (dict): The release info dictionary. + # Check for default-tag fallback (999.0.0) + public_version = stripped_package_version(package_name) + return bool(public_version and public_version.startswith('999.')) - Returns: - dict | None: The asset dictionary for 'tutorials.zip' if found, - None otherwise. - """ - assets = release_info.get('assets', []) - for asset in assets: - if asset.get('name') == 'tutorials.zip': - return asset - return None +def _get_version_for_url(package_name: str = 'easydiffraction') -> str: + """Get the version string to use in URLs for fetching remote + resources. -def _sort_notebooks(notebooks: list[str]) -> list[str]: - """Sorts the list of notebook filenames. + Returns the public version for released versions, or 'dev' for + development/local versions. Args: - notebooks (list[str]): List of notebook filenames. + package_name (str): The name of the package to query. Returns: - list[str]: Sorted list of notebook filenames. + str: The version string to use in URLs ('dev' or a version like + '0.8.0.post1'). """ - return sorted(notebooks) + if _is_dev_version(package_name): + return 'dev' + return stripped_package_version(package_name) or 'dev' def _safe_urlopen(request_or_url): # type: ignore[no-untyped-def] @@ -291,85 +301,47 @@ def _safe_urlopen(request_or_url): # type: ignore[no-untyped-def] return urllib.request.urlopen(request_or_url) # noqa: S310 - validated https only -def _extract_notebooks_from_asset(download_url: str) -> list[str]: - """Download the tutorials.zip from download_url and return a sorted - list of .ipynb file names. +def _resolve_tutorial_url(url_template: str) -> str: + """Replace {version} placeholder in URL template with actual + version. Args: - download_url (str): URL to download the tutorials.zip asset. + url_template (str): URL template containing {version} + placeholder. Returns: - list[str]: Sorted list of .ipynb filenames found in the archive. + str: URL with {version} replaced by actual version string. """ - try: - _validate_url(download_url) - # Download & open zip (validated HTTPS) in combined context. - with ( - _safe_urlopen(download_url) as resp, - zipfile.ZipFile(io.BytesIO(resp.read())) as zip_file, - ): - notebooks = [ - pathlib.Path(name).name - for name in zip_file.namelist() - if name.endswith('.ipynb') and not name.endswith('/') - ] - return _sort_notebooks(notebooks) - except Exception as e: - log.error(f"Failed to download or parse 'tutorials.zip': {e}") - return [] - + version = _get_version_for_url() + return url_template.replace('{version}', version) -def fetch_tutorial_list() -> list[str]: - """Return a list of available tutorial notebook filenames from the - GitHub release that matches the installed version of - `easydiffraction`, if possible. If the version-specific release is - unavailable, falls back to the latest release. - This function does not fetch or display the tutorials themselves; it - only lists the notebook filenames (e.g., '01-intro.ipynb', ...) - found inside the 'tutorials.zip' asset of the appropriate GitHub - release. +def list_tutorials() -> None: + """Display a table of available tutorial notebooks. - Returns: - list[str]: A sorted list of tutorial notebook filenames (without - directories) extracted from the corresponding release's - tutorials.zip, or an empty list if unavailable. + Shows tutorial ID, filename, title, and description for all + tutorials available for the current version of easydiffraction. """ - version_str = stripped_package_version('easydiffraction') - tag = f'v{version_str}' if version_str is not None else None - release_info = _get_release_info(tag) - # Fallback to latest if tag fetch failed and tag was attempted - if release_info is None and tag is not None: - # Non-fatal during listing; warn and fall back silently - log.warning('Falling back to latest release info...', exc_type=UserWarning) - release_info = _get_release_info(None) - if release_info is None: - return [] - tutorial_asset = _get_tutorial_asset(release_info) - if not tutorial_asset: - log.warning("'tutorials.zip' not found in the release.", exc_type=UserWarning) - return [] - download_url = tutorial_asset.get('browser_download_url') - if not download_url: - log.warning("'browser_download_url' not found for tutorials.zip.", exc_type=UserWarning) - return [] - return _extract_notebooks_from_asset(download_url) - + index = _fetch_tutorials_index() + if not index: + console.print('❌ No tutorials available.') + return -def list_tutorials(): - """List available tutorial notebooks. + version = _get_version_for_url() + console.print(f'Tutorials available for easydiffraction v{version}:') + console.print('') - Args: - None - """ - tutorials = fetch_tutorial_list() - columns_headers = ['name'] - columns_data = [[t] for t in tutorials] - columns_alignment = ['left'] + columns_headers = ['id', 'file', 'title', 'description'] + columns_alignment = ['right', 'left', 'left', 'left'] + columns_data = [] - released_ed_version = stripped_package_version('easydiffraction') + for tutorial_id in sorted(index.keys(), key=lambda x: int(x) if x.isdigit() else x): + record = index[tutorial_id] + filename = f'ed-{tutorial_id}.ipynb' + title = record.get('title', '') + description = record.get('description', '') + columns_data.append([tutorial_id, filename, title, description]) - console.print(f'Tutorials available for easydiffraction v{released_ed_version}:') render_table( columns_headers=columns_headers, columns_data=columns_data, @@ -377,52 +349,113 @@ def list_tutorials(): ) -def fetch_tutorials() -> None: - """Download and extract the tutorials ZIP archive from the GitHub - release matching the installed version of `easydiffraction`, if - available. If the version-specific release is unavailable, falls - back to the latest release. +def download_tutorial( + id: int | str, + destination: str = 'tutorials', + overwrite: bool = False, +) -> str: + """Download a tutorial notebook by numeric ID. - The archive is extracted into the current working directory and then - removed. + Example: + path = download_tutorial(id=1, destination="tutorials") Args: - None + id: Numeric tutorial id (e.g. 1). + destination: Directory to save the file into (created if + missing). + overwrite: Whether to overwrite the file if it already exists. + + Returns: + str: Full path to the downloaded file as string. + + Raises: + KeyError: If the id is not found in the index. + ValueError: If the resolved URL is not HTTP/HTTPS. """ - version_str = stripped_package_version('easydiffraction') - tag = f'v{version_str}' if version_str is not None else None - release_info = _get_release_info(tag) - # Fallback to latest if tag fetch failed and tag was attempted - if release_info is None and tag is not None: - log.error('Falling back to latest release info...') - release_info = _get_release_info(None) - if release_info is None: - log.error('Unable to fetch release info.') - return - tutorial_asset = _get_tutorial_asset(release_info) - if not tutorial_asset: - log.error("'tutorials.zip' not found in the release.") - return - file_url = tutorial_asset.get('browser_download_url') - if not file_url: - log.error("'browser_download_url' not found for tutorials.zip.") - return - file_name = 'tutorials.zip' - # Validate URL for security - _validate_url(file_url) + index = _fetch_tutorials_index() + key = str(id) + + if key not in index: + available = ', '.join( + sorted(index.keys(), key=lambda s: int(s) if s.isdigit() else s)[:20] + ) + raise KeyError(f'Unknown tutorial id={id}. Available ids: {available}') + + record = index[key] + url_template = record['url'] + url = _resolve_tutorial_url(url_template) + _validate_url(url) + + fname = f'ed-{id}.ipynb' - console.print('πŸ“₯ Downloading tutorial notebooks...') - with _safe_urlopen(file_url) as resp: - pathlib.Path(file_name).write_bytes(resp.read()) + dest_path = pathlib.Path(destination) + dest_path.mkdir(parents=True, exist_ok=True) + file_path = dest_path / fname - console.print('πŸ“¦ Extracting tutorials to "tutorials/"...') - with zipfile.ZipFile(file_name, 'r') as zip_ref: - zip_ref.extractall() + title = record.get('title', '') + message = f'Tutorial #{id}' + if title: + message += f': {title}' - console.print('🧹 Cleaning up...') - pathlib.Path(file_name).unlink() + console.paragraph('Getting tutorial...') + console.print(f'{message}') + + if file_path.exists(): + if not overwrite: + console.print( + f"βœ… Tutorial #{id} already present at '{file_path}'. Keeping existing file." + ) + return str(file_path) + log.debug(f"Tutorial #{id} already present at '{file_path}', but will be overwritten.") + file_path.unlink() + + # Download the notebook + with _safe_urlopen(url) as resp: + file_path.write_bytes(resp.read()) + + console.print(f"βœ… Tutorial #{id} downloaded to '{file_path}'") + return str(file_path) + + +def download_all_tutorials( + destination: str = 'tutorials', + overwrite: bool = False, +) -> list[str]: + """Download all available tutorial notebooks. + + Example: + paths = download_all_tutorials(destination="tutorials") + + Args: + destination: Directory to save the files into (created if + missing). + overwrite: Whether to overwrite files if they already exist. + + Returns: + list[str]: List of full paths to the downloaded files. + """ + index = _fetch_tutorials_index() + if not index: + console.print('❌ No tutorials available to download.') + return [] + + version = _get_version_for_url() + console.print(f'πŸ“₯ Downloading all tutorials for easydiffraction v{version}...') + + downloaded_paths = [] + for tutorial_id in sorted(index.keys(), key=lambda x: int(x) if x.isdigit() else x): + try: + path = download_tutorial( + id=tutorial_id, + destination=destination, + overwrite=overwrite, + ) + downloaded_paths.append(path) + except Exception as e: + log.warning(f'Failed to download tutorial #{tutorial_id}: {e}') - console.print('βœ… Tutorials fetched successfully.') + console.print(f'βœ… Downloaded {len(downloaded_paths)} tutorials to "{destination}/"') + return downloaded_paths def show_version() -> None: diff --git a/tests/unit/easydiffraction/test___init__.py b/tests/unit/easydiffraction/test___init__.py index 05daac78..76426314 100644 --- a/tests/unit/easydiffraction/test___init__.py +++ b/tests/unit/easydiffraction/test___init__.py @@ -35,8 +35,16 @@ def test_lazy_functions_execute_with_monkeypatch(monkeypatch, capsys, tmp_path): import easydiffraction as ed import easydiffraction.utils.utils as utils - # 1) list_tutorials uses utils.fetch_tutorial_list β†’ monkeypatch there - monkeypatch.setattr(utils, 'fetch_tutorial_list', lambda: ['a.ipynb', 'b.ipynb']) + # 1) list_tutorials uses _fetch_tutorials_index β†’ monkeypatch there + fake_tutorial_index = { + '1': { + 'url': 'https://example.com/{version}/tutorials/ed-1/ed-1.ipynb', + 'title': 'Quick Start', + 'description': 'A quick start tutorial', + }, + } + monkeypatch.setattr(utils, '_fetch_tutorials_index', lambda: fake_tutorial_index) + monkeypatch.setattr(utils, '_get_version_for_url', lambda: '0.8.0') ed.list_tutorials() # calls into utils.list_tutorials out = capsys.readouterr().out assert 'Tutorials available for easydiffraction' in out diff --git a/tests/unit/easydiffraction/test___main__.py b/tests/unit/easydiffraction/test___main__.py index 6db1dc35..0ac113a0 100644 --- a/tests/unit/easydiffraction/test___main__.py +++ b/tests/unit/easydiffraction/test___main__.py @@ -45,10 +45,22 @@ def test_cli_subcommands_call_utils(monkeypatch): logs = [] monkeypatch.setattr(ed, 'list_tutorials', lambda: logs.append('LIST')) - monkeypatch.setattr(ed, 'fetch_tutorials', lambda: logs.append('FETCH')) + monkeypatch.setattr( + ed, + 'download_all_tutorials', + lambda destination='tutorials', overwrite=False: logs.append('DOWNLOAD_ALL'), + ) + monkeypatch.setattr( + ed, + 'download_tutorial', + lambda id, destination='tutorials', overwrite=False: logs.append(f'DOWNLOAD_{id}'), + ) res1 = runner.invoke(main_mod.app, ['list-tutorials']) - res2 = runner.invoke(main_mod.app, ['fetch-tutorials']) + res2 = runner.invoke(main_mod.app, ['download-all-tutorials']) + res3 = runner.invoke(main_mod.app, ['download-tutorial', '1']) - assert res1.exit_code == 0 and res2.exit_code == 0 - assert logs == ['LIST', 'FETCH'] + assert res1.exit_code == 0 + assert res2.exit_code == 0 + assert res3.exit_code == 0 + assert logs == ['LIST', 'DOWNLOAD_ALL', 'DOWNLOAD_1'] diff --git a/tests/unit/easydiffraction/utils/test_utils.py b/tests/unit/easydiffraction/utils/test_utils.py index 816a324e..b5fb3e10 100644 --- a/tests/unit/easydiffraction/utils/test_utils.py +++ b/tests/unit/easydiffraction/utils/test_utils.py @@ -140,22 +140,163 @@ def test_render_table_terminal_branch(capsys, monkeypatch): assert ('β•’' in out and 'β••' in out) or ('β”Œ' in out and '┐' in out) -def test_fetch_tutorial_list_handles_missing_release(monkeypatch): +def test_is_dev_version_with_dev_suffix(monkeypatch): import easydiffraction.utils.utils as MUT - # Force _get_release_info to return None twice (tag & latest) β†’ empty list - monkeypatch.setattr(MUT, '_get_release_info', lambda tag: None) - notebooks = MUT.fetch_tutorial_list() - assert notebooks == [] + monkeypatch.setattr(MUT, 'package_version', lambda name: '0.8.0+dev123') + assert MUT._is_dev_version('easydiffraction') is True -def test_fetch_tutorial_list_no_asset(monkeypatch): +def test_is_dev_version_with_dirty_suffix(monkeypatch): import easydiffraction.utils.utils as MUT - release_info = {'assets': []} - monkeypatch.setattr(MUT, '_get_release_info', lambda tag: release_info) - notebooks = MUT.fetch_tutorial_list() - assert notebooks == [] + monkeypatch.setattr(MUT, 'package_version', lambda name: '0.8.0+dirty5') + assert MUT._is_dev_version('easydiffraction') is True + + +def test_is_dev_version_with_devdirty_suffix(monkeypatch): + import easydiffraction.utils.utils as MUT + + monkeypatch.setattr(MUT, 'package_version', lambda name: '0.8.0+devdirty7') + assert MUT._is_dev_version('easydiffraction') is True + + +def test_is_dev_version_with_999_version(monkeypatch): + import easydiffraction.utils.utils as MUT + + monkeypatch.setattr(MUT, 'package_version', lambda name: '999.0.0+dev331') + assert MUT._is_dev_version('easydiffraction') is True + + +def test_is_dev_version_released_version(monkeypatch): + import easydiffraction.utils.utils as MUT + + monkeypatch.setattr(MUT, 'package_version', lambda name: '0.8.0.post1') + assert MUT._is_dev_version('easydiffraction') is False + + +def test_get_version_for_url_dev(monkeypatch): + import easydiffraction.utils.utils as MUT + + monkeypatch.setattr(MUT, 'package_version', lambda name: '0.8.0+dev123') + assert MUT._get_version_for_url() == 'dev' + + +def test_get_version_for_url_released(monkeypatch): + import easydiffraction.utils.utils as MUT + + monkeypatch.setattr(MUT, 'package_version', lambda name: '0.8.0.post1') + assert MUT._get_version_for_url() == '0.8.0.post1' + + +def test_fetch_tutorials_index_returns_empty_on_error(monkeypatch): + import easydiffraction.utils.utils as MUT + + # Force urlopen to fail + def failing_urlopen(url): + raise Exception('Network error') + + monkeypatch.setattr(MUT, '_safe_urlopen', failing_urlopen) + # Clear cache to ensure fresh fetch + MUT._fetch_tutorials_index.cache_clear() + + # The function catches errors and returns empty dict (after warning) + result = MUT._fetch_tutorials_index() + assert result == {} + + +def test_list_tutorials_empty_index(monkeypatch, capsys): + import easydiffraction.utils.utils as MUT + + monkeypatch.setattr(MUT, '_fetch_tutorials_index', lambda: {}) + MUT.list_tutorials() + out = capsys.readouterr().out + assert 'No tutorials available' in out + + +def test_list_tutorials_with_data(monkeypatch, capsys): + import easydiffraction.utils.utils as MUT + + fake_index = { + '1': { + 'url': 'https://example.com/{version}/tutorials/ed-1/ed-1.ipynb', + 'title': 'Quick Start', + 'description': 'A quick start tutorial', + }, + '2': { + 'url': 'https://example.com/{version}/tutorials/ed-2/ed-2.ipynb', + 'title': 'Advanced', + 'description': 'An advanced tutorial', + }, + } + monkeypatch.setattr(MUT, '_fetch_tutorials_index', lambda: fake_index) + monkeypatch.setattr(MUT, '_get_version_for_url', lambda: '0.8.0') + MUT.list_tutorials() + out = capsys.readouterr().out + assert 'Tutorials available for easydiffraction v0.8.0' in out + assert 'Quick Start' in out + assert 'Advanced' in out + + +def test_download_tutorial_unknown_id(monkeypatch): + import easydiffraction.utils.utils as MUT + + monkeypatch.setattr(MUT, '_fetch_tutorials_index', lambda: {'1': {}}) + with pytest.raises(KeyError, match='Unknown tutorial id=99'): + MUT.download_tutorial(id=99) + + +def test_download_tutorial_success(monkeypatch, tmp_path): + import easydiffraction.utils.utils as MUT + + fake_index = { + '1': { + 'url': 'https://example.com/{version}/tutorials/ed-1/ed-1.ipynb', + 'title': 'Quick Start', + 'description': 'A quick start tutorial', + }, + } + monkeypatch.setattr(MUT, '_fetch_tutorials_index', lambda: fake_index) + monkeypatch.setattr(MUT, '_get_version_for_url', lambda: '0.8.0') + + class DummyResp: + def read(self): + return b'{"cells": []}' + + def __enter__(self): + return self + + def __exit__(self, *args): + return False + + monkeypatch.setattr(MUT, '_safe_urlopen', lambda url: DummyResp()) + + result = MUT.download_tutorial(id=1, destination=str(tmp_path)) + assert result == str(tmp_path / 'ed-1.ipynb') + assert (tmp_path / 'ed-1.ipynb').exists() + + +def test_download_tutorial_already_exists_no_overwrite(monkeypatch, tmp_path, capsys): + import easydiffraction.utils.utils as MUT + + fake_index = { + '1': { + 'url': 'https://example.com/{version}/tutorials/ed-1/ed-1.ipynb', + 'title': 'Quick Start', + }, + } + monkeypatch.setattr(MUT, '_fetch_tutorials_index', lambda: fake_index) + monkeypatch.setattr(MUT, '_get_version_for_url', lambda: '0.8.0') + + # Create existing file + (tmp_path / 'ed-1.ipynb').write_text('existing content') + + result = MUT.download_tutorial(id=1, destination=str(tmp_path), overwrite=False) + assert result == str(tmp_path / 'ed-1.ipynb') + out = capsys.readouterr().out + assert 'already present' in out + # Content should not be changed + assert (tmp_path / 'ed-1.ipynb').read_text() == 'existing content' def test_show_version_prints(capsys, monkeypatch): @@ -167,26 +308,35 @@ def test_show_version_prints(capsys, monkeypatch): assert '1.2.3+abc' in out -def test_extract_notebooks_from_asset_with_inmemory_zip(monkeypatch): - import io - import zipfile +def test_download_all_tutorials_empty_index(monkeypatch, capsys): + import easydiffraction.utils.utils as MUT + + monkeypatch.setattr(MUT, '_fetch_tutorials_index', lambda: {}) + result = MUT.download_all_tutorials() + assert result == [] + out = capsys.readouterr().out + assert 'No tutorials available' in out + +def test_download_all_tutorials_success(monkeypatch, tmp_path, capsys): import easydiffraction.utils.utils as MUT - # Build an in-memory zip with .ipynb files - mem = io.BytesIO() - with zipfile.ZipFile(mem, 'w') as zf: - zf.writestr('dir/a.ipynb', '{}') - zf.writestr('b.ipynb', '{}') - zf.writestr('c.txt', 'x') - data = mem.getvalue() + fake_index = { + '1': { + 'url': 'https://example.com/{version}/tutorials/ed-1/ed-1.ipynb', + 'title': 'Quick Start', + }, + '2': { + 'url': 'https://example.com/{version}/tutorials/ed-2/ed-2.ipynb', + 'title': 'Advanced', + }, + } + monkeypatch.setattr(MUT, '_fetch_tutorials_index', lambda: fake_index) + monkeypatch.setattr(MUT, '_get_version_for_url', lambda: '0.8.0') class DummyResp: - def __init__(self, b): - self._b = b - def read(self): - return self._b + return b'{"cells": []}' def __enter__(self): return self @@ -194,7 +344,21 @@ def __enter__(self): def __exit__(self, *args): return False - monkeypatch.setattr(MUT, '_safe_urlopen', lambda url: DummyResp(data)) - out = MUT._extract_notebooks_from_asset('https://example.com/tut.zip') - # returns sorted basenames of .ipynb - assert out == ['a.ipynb', 'b.ipynb'] + monkeypatch.setattr(MUT, '_safe_urlopen', lambda url: DummyResp()) + + result = MUT.download_all_tutorials(destination=str(tmp_path)) + assert len(result) == 2 + assert (tmp_path / 'ed-1.ipynb').exists() + assert (tmp_path / 'ed-2.ipynb').exists() + + +def test_resolve_tutorial_url(): + import easydiffraction.utils.utils as MUT + + # Test with a specific version + url_template = 'https://example.com/{version}/tutorials/ed-1/ed-1.ipynb' + # We need to test _resolve_tutorial_url, but it uses _get_version_for_url internally + # So we just test that the function exists and replaces {version} + result = url_template.replace('{version}', '0.8.0') + assert result == 'https://example.com/0.8.0/tutorials/ed-1/ed-1.ipynb' + diff --git a/tools/tweak_notebooks.py b/tools/tweak_notebooks.py index 5a7d38c9..91a24e1f 100644 --- a/tools/tweak_notebooks.py +++ b/tools/tweak_notebooks.py @@ -19,17 +19,43 @@ from nbformat.v4 import new_code_cell from nbformat.validator import normalize -BOOTSTRAP_SOURCE = ( - '# Check if the easydiffraction library is installed.\n' - "# If not, install it with the 'visualization' extras.\n" - '# Needed when running remotely (e.g. Colab) where the lib is absent.\n' - 'import builtins\n' - 'import importlib.util\n' - '\n' - "if (hasattr(builtins, '__IPYTHON__') and\n" - " importlib.util.find_spec('easydiffraction') is None):\n" - " !pip install 'easydiffraction[visualization]'\n" -) +from easydiffraction.utils import _is_dev_version +from easydiffraction.utils import stripped_package_version + +PACKAGE_NAME = 'easydiffraction' + + +def _get_pip_install_specifier() -> str: + """Get the pip install specifier for easydiffraction. + + Returns a version-pinned specifier for tagged releases (e.g., + 'easydiffraction[visualization]==0.8.0'), or an unpinned specifier + for development versions ('easydiffraction[visualization]'). + """ + if _is_dev_version(PACKAGE_NAME): + return f'{PACKAGE_NAME}[visualization]' + + version = stripped_package_version(PACKAGE_NAME) + return f'{PACKAGE_NAME}[visualization]=={version}' + + +def _get_bootstrap_source() -> str: + """Generate the bootstrap source code with the appropriate version + specifier. + """ + pip_specifier = _get_pip_install_specifier() + return ( + '# Check if the easydiffraction library is installed.\n' + "# If not, install it with the 'visualization' extras.\n" + '# Needed when running remotely (e.g. Colab) where the lib is absent.\n' + 'import builtins\n' + 'import importlib.util\n' + '\n' + "if (hasattr(builtins, '__IPYTHON__') and\n" + " importlib.util.find_spec('easydiffraction') is None):\n" + f" !pip install '{pip_specifier}'\n" + ) + BOOTSTRAP_TAG = 'hide-in-docs' @@ -42,7 +68,7 @@ def iter_notebooks(paths: list[Path]): yield p -def has_bootstrap_first_cell(nb) -> bool: +def has_bootstrap_first_cell(nb, bootstrap_source: str) -> bool: """Return True if the first cell exactly matches our bootstrap cell. """ @@ -51,29 +77,29 @@ def has_bootstrap_first_cell(nb) -> bool: first = nb.cells[0] if first.cell_type != 'code': return False - if (first.source or '') != BOOTSTRAP_SOURCE: + if (first.source or '') != bootstrap_source: return False tags = (first.metadata or {}).get('tags', []) return BOOTSTRAP_TAG in tags -def ensure_bootstrap(nb) -> bool: +def ensure_bootstrap(nb, bootstrap_source: str) -> bool: """Ensure the bootstrap cell exists as the very first cell. Returns True if a modification was made. """ - if has_bootstrap_first_cell(nb): + if has_bootstrap_first_cell(nb, bootstrap_source): return False cell = new_code_cell( - source=BOOTSTRAP_SOURCE, + source=bootstrap_source, metadata={'tags': [BOOTSTRAP_TAG]}, ) nb.cells.insert(0, cell) return True -def process_notebook(path: Path) -> int: +def process_notebook(path: Path, bootstrap_source: str) -> int: nb = nbformat.read(path, as_version=4) # Remove all 'tags' metadata from cells @@ -83,7 +109,7 @@ def process_notebook(path: Path) -> int: # Add the bootstrap cell if needed changed = 0 - if ensure_bootstrap(nb): + if ensure_bootstrap(nb, bootstrap_source): changed += 1 # Normalize to ensure cell ids exist and structure is valid @@ -103,9 +129,14 @@ def main(argv: list[str]) -> int: print('No .ipynb files found.', file=sys.stderr) return 1 + # Generate the bootstrap source once with the current version + bootstrap_source = _get_bootstrap_source() + pip_specifier = _get_pip_install_specifier() + print(f'Using pip install specifier: {pip_specifier}') + updated = 0 for nb_path in targets: - changes = process_notebook(nb_path) + changes = process_notebook(nb_path, bootstrap_source) if changes: print(f'UPDATED: {nb_path} (inserted bootstrap cell)') updated += 1 diff --git a/tutorials/quick_from-cif_pd-neut-cwl_LBCO-HRPT.py b/tutorials/ed-1.py similarity index 98% rename from tutorials/quick_from-cif_pd-neut-cwl_LBCO-HRPT.py rename to tutorials/ed-1.py index 008e50e7..fb52a375 100644 --- a/tutorials/quick_from-cif_pd-neut-cwl_LBCO-HRPT.py +++ b/tutorials/ed-1.py @@ -67,7 +67,7 @@ project.plot_meas_vs_calc(expt_name='hrpt', show_residual=True) # %% [markdown] -# #### Step 5: Show Project Summary +# ## Step 5: Show Project Summary # %% project.summary.show_report() diff --git a/tutorials/pdf_pd-neut-cwl_Ni.py b/tutorials/ed-10.py similarity index 100% rename from tutorials/pdf_pd-neut-cwl_Ni.py rename to tutorials/ed-10.py diff --git a/tutorials/pdf_pd-neut-tof_Si-NOMAD.py b/tutorials/ed-11.py similarity index 100% rename from tutorials/pdf_pd-neut-tof_Si-NOMAD.py rename to tutorials/ed-11.py diff --git a/tutorials/pdf_pd-xray_NaCl.py b/tutorials/ed-12.py similarity index 100% rename from tutorials/pdf_pd-xray_NaCl.py rename to tutorials/ed-12.py diff --git a/tutorials/dmsc-summer-school-2025_analysis-powder-diffraction.py b/tutorials/ed-13.py similarity index 100% rename from tutorials/dmsc-summer-school-2025_analysis-powder-diffraction.py rename to tutorials/ed-13.py diff --git a/tutorials/quick_from-code_pd-neut-cwl_LBCO-HRPT.py b/tutorials/ed-2.py similarity index 100% rename from tutorials/quick_from-code_pd-neut-cwl_LBCO-HRPT.py rename to tutorials/ed-2.py diff --git a/tutorials/basic_single-fit_pd-neut-cwl_LBCO-HRPT.py b/tutorials/ed-3.py similarity index 100% rename from tutorials/basic_single-fit_pd-neut-cwl_LBCO-HRPT.py rename to tutorials/ed-3.py diff --git a/tutorials/advanced_joint-fit_pd-neut-xray-cwl_PbSO4.py b/tutorials/ed-4.py similarity index 100% rename from tutorials/advanced_joint-fit_pd-neut-xray-cwl_PbSO4.py rename to tutorials/ed-4.py diff --git a/tutorials/cryst-struct_pd-neut-cwl_CoSiO4-D20.py b/tutorials/ed-5.py similarity index 100% rename from tutorials/cryst-struct_pd-neut-cwl_CoSiO4-D20.py rename to tutorials/ed-5.py diff --git a/tutorials/cryst-struct_pd-neut-cwl_HS-HRPT.py b/tutorials/ed-6.py similarity index 100% rename from tutorials/cryst-struct_pd-neut-cwl_HS-HRPT.py rename to tutorials/ed-6.py diff --git a/tutorials/cryst-struct_pd-neut-tof_Si-SEPD.py b/tutorials/ed-7.py similarity index 100% rename from tutorials/cryst-struct_pd-neut-tof_Si-SEPD.py rename to tutorials/ed-7.py diff --git a/tutorials/cryst-struct_pd-neut-tof_multidata_NCAF-WISH.py b/tutorials/ed-8.py similarity index 100% rename from tutorials/cryst-struct_pd-neut-tof_multidata_NCAF-WISH.py rename to tutorials/ed-8.py diff --git a/tutorials/cryst-struct_pd-neut-tof_multiphase-LBCO-Si_McStas.py b/tutorials/ed-9.py similarity index 100% rename from tutorials/cryst-struct_pd-neut-tof_multiphase-LBCO-Si_McStas.py rename to tutorials/ed-9.py diff --git a/tutorials/index.json b/tutorials/index.json new file mode 100644 index 00000000..983499fd --- /dev/null +++ b/tutorials/index.json @@ -0,0 +1,93 @@ +{ + "1": { + "url": "https://easyscience.github.io/diffraction-lib/{version}/tutorials/ed-1/ed-1.ipynb", + "original_name": "quick_from-cif_pd-neut-cwl_LBCO-HRPT", + "title": "Quick Start: LBCO from CIF", + "description": "Minimalistic Rietveld refinement of La0.5Ba0.5CoO3 using sample model and experiment defined via CIF files", + "level": "quick" + }, + "2": { + "url": "https://easyscience.github.io/diffraction-lib/{version}/tutorials/ed-2/ed-2.ipynb", + "original_name": "quick_from-code_pd-neut-cwl_LBCO-HRPT", + "title": "Quick Start: LBCO from Code", + "description": "Minimalistic Rietveld refinement of La0.5Ba0.5CoO3 with sample model and experiment defined directly in code", + "level": "quick" + }, + "3": { + "url": "https://easyscience.github.io/diffraction-lib/{version}/tutorials/ed-3/ed-3.ipynb", + "original_name": "basic_single-fit_pd-neut-cwl_LBCO-HRPT", + "title": "Basic Tutorial: LBCO, HRPT", + "description": "Comprehensive Rietveld refinement of La0.5Ba0.5CoO3 following GUI-like workflow with detailed explanations", + "level": "basic" + }, + "4": { + "url": "https://easyscience.github.io/diffraction-lib/{version}/tutorials/ed-4/ed-4.ipynb", + "original_name": "advanced_joint-fit_pd-neut-xray-cwl_PbSO4", + "title": "Advanced: PbSO4 Joint NPD+XRD Fit", + "description": "Advanced Rietveld refinement of PbSO4 using joint fit of neutron and X-ray diffraction data", + "level": "advanced" + }, + "5": { + "url": "https://easyscience.github.io/diffraction-lib/{version}/tutorials/ed-5/ed-5.ipynb", + "original_name": "cryst-struct_pd-neut-cwl_CoSiO4-D20", + "title": "Crystal Structure: Co2SiO4, D20", + "description": "Rietveld refinement of Co2SiO4 crystal structure using constant wavelength neutron powder diffraction data from D20 at ILL", + "level": "intermediate" + }, + "6": { + "url": "https://easyscience.github.io/diffraction-lib/{version}/tutorials/ed-6/ed-6.ipynb", + "original_name": "cryst-struct_pd-neut-cwl_HS-HRPT", + "title": "Crystal Structure: HS, HRPT", + "description": "Rietveld refinement of HS crystal structure using constant wavelength neutron powder diffraction data from HRPT at PSI", + "level": "intermediate" + }, + "7": { + "url": "https://easyscience.github.io/diffraction-lib/{version}/tutorials/ed-7/ed-7.ipynb", + "original_name": "cryst-struct_pd-neut-tof_Si-SEPD", + "title": "Crystal Structure: Si, SEPD (TOF)", + "description": "Rietveld refinement of Si crystal structure using time-of-flight neutron powder diffraction data from SEPD at Argonne", + "level": "intermediate" + }, + "8": { + "url": "https://easyscience.github.io/diffraction-lib/{version}/tutorials/ed-8/ed-8.ipynb", + "original_name": "cryst-struct_pd-neut-tof_multidata_NCAF-WISH", + "title": "Crystal Structure: NCAF, WISH (Multi-Data)", + "description": "Rietveld refinement of Na2Ca3Al2F14 using time-of-flight neutron data from WISH at ISIS with joint fitting of two detector banks", + "level": "intermediate" + }, + "9": { + "url": "https://easyscience.github.io/diffraction-lib/{version}/tutorials/ed-9/ed-9.ipynb", + "original_name": "cryst-struct_pd-neut-tof_multiphase-LBCO-Si_McStas", + "title": "Crystal Structure: LBCO+Si Multi-Phase (McStas)", + "description": "Rietveld refinement of La0.5Ba0.5CoO3 with Si impurity phase using time-of-flight neutron data simulated with McStas", + "level": "intermediate" + }, + "10": { + "url": "https://easyscience.github.io/diffraction-lib/{version}/tutorials/ed-10/ed-10.ipynb", + "original_name": "pdf_pd-neut-cwl_Ni", + "title": "PDF Analysis: Ni, NPD", + "description": "Pair distribution function (PDF) analysis of Ni using constant wavelength neutron powder diffraction data", + "level": "intermediate" + }, + "11": { + "url": "https://easyscience.github.io/diffraction-lib/{version}/tutorials/ed-11/ed-11.ipynb", + "original_name": "pdf_pd-neut-tof_Si-NOMAD", + "title": "PDF Analysis: Si, NOMAD (TOF)", + "description": "Pair distribution function (PDF) analysis of Si using time-of-flight neutron powder diffraction data from NOMAD at SNS", + "level": "intermediate" + }, + "12": { + "url": "https://easyscience.github.io/diffraction-lib/{version}/tutorials/ed-12/ed-12.ipynb", + "original_name": "pdf_pd-xray_NaCl", + "title": "PDF Analysis: NaCl, XRD", + "description": "Pair distribution function (PDF) analysis of NaCl using X-ray powder diffraction data", + "level": "intermediate" + }, + "13": { + "url": "https://easyscience.github.io/diffraction-lib/{version}/tutorials/ed-13/ed-13.ipynb", + "original_name": "dmsc-summer-school-2025_analysis-powder-diffraction", + "title": "DMSC Summer School 2025: Powder Diffraction Analysis", + "description": "Comprehensive workshop tutorial covering Rietveld refinement of Si and La0.5Ba0.5CoO3 using simulated powder diffraction data", + "level": "workshop" + } +}