From aeabd18a1226afb98a963ada94347eaa5e3b2888 Mon Sep 17 00:00:00 2001 From: Zain Sohail Date: Mon, 15 Jul 2024 18:45:53 +0200 Subject: [PATCH 01/18] add all doc files for pydata theme --- docs/conf.py | 30 +++++++++++-- docs/getting_started.rst | 2 - docs/index.md | 50 ++++++++++++++++++++++ docs/index.rst | 44 -------------------- docs/misc/contributing.rst | 3 +- docs/misc/contribution.md | 8 ++++ docs/misc/maintain.rst | 2 +- docs/sed/api.rst | 17 ++++++++ docs/sed/config.rst | 31 -------------- docs/sed/dataset.rst | 2 +- docs/user_guide/config.md | 29 +++++++++++++ docs/user_guide/index.md | 25 +++++++++++ docs/user_guide/installation.md | 74 +++++++++++++++++++++++++++++++++ docs/workflows/index.md | 15 +++++++ 14 files changed, 248 insertions(+), 84 deletions(-) delete mode 100644 docs/getting_started.rst create mode 100644 docs/index.md delete mode 100644 docs/index.rst create mode 100644 docs/misc/contribution.md create mode 100644 docs/sed/api.rst create mode 100644 docs/user_guide/config.md create mode 100644 docs/user_guide/index.md create mode 100644 docs/user_guide/installation.md create mode 100644 docs/workflows/index.md diff --git a/docs/conf.py b/docs/conf.py index bd4c1396..68ec181c 100644 --- a/docs/conf.py +++ b/docs/conf.py @@ -25,8 +25,9 @@ def _get_project_meta(): return tomlkit.parse(file_contents)["tool"]["poetry"] +# -- Project information ----------------------------------------------------- pkg_meta = _get_project_meta() -project = str(pkg_meta["name"]) +project = "SED" copyright = "2024, OpenCOMPES team" author = "OpenCOMPES team" @@ -41,12 +42,12 @@ 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.viewcode", "sphinx.ext.coverage", "sphinx_autodoc_typehints", "bokeh.sphinxext.bokeh_autodoc", @@ -56,6 +57,8 @@ def _get_project_meta(): ] +exclude_patterns = ["_build", "Thumbs.db", ".DS_Store", "**.ipynb_checkpoints"] + autoclass_content = "class" autodoc_member_order = "bysource" @@ -98,7 +101,28 @@ 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/sed", + "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/sed/switcher.json", + "version_match": version, + }, + "content_footer_items": ["last-updated"], +} + +html_context = { + "github_user": "OpenCOMPES", + "github_repo": "sed", + "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/getting_started.rst b/docs/getting_started.rst deleted file mode 100644 index fba01724..00000000 --- a/docs/getting_started.rst +++ /dev/null @@ -1,2 +0,0 @@ -.. include:: ../README.md - :parser: myst_parser.sphinx_ diff --git a/docs/index.md b/docs/index.md new file mode 100644 index 00000000..0f368f80 --- /dev/null +++ b/docs/index.md @@ -0,0 +1,50 @@ +--- +myst: + html_meta: + "description lang=en": | + Top-level documentation for sed, with links to the rest + of the site.. +html_theme.sidebar_secondary.remove: true +--- + +# SED documentation + +SED (Single Event Data Frame) is a collection of routines and utilities to handle photoelectron resolved datastreams. +It features lazy evaluation of dataframe processing using dask, numba-accelerated multi-dimensional binning, calibration and correction for trARPES (Time- and angle-resolved photoemission spectroscopy) datasets. +The package ensures provenance and FAIR data through metadata tracking, usage of the community defined NeXus format. + +```{toctree} +:maxdepth: 2 + +user_guide/index + +``` + +## Examples + +Several example notebooks to demonstrate the functionality of SED for end-to-end data analysis workflows. + +```{toctree} +:maxdepth: 2 + +workflows/index +``` + +## API + +```{toctree} +:maxdepth: 2 + +sed/api +``` + + +## Community and contribution guide + +Information about the community behind this theme and how you can contribute. + +```{toctree} +:maxdepth: 2 + +misc/contribution +``` diff --git a/docs/index.rst b/docs/index.rst deleted file mode 100644 index b61dcb31..00000000 --- a/docs/index.rst +++ /dev/null @@ -1,44 +0,0 @@ -Single-Event DataFrame (SED) documentation -================================================ - -.. toctree:: - :maxdepth: 1 - :caption: Getting Started - - getting_started - tutorial/1_binning_fake_data - tutorial/2_conversion_pipeline_for_example_time-resolved_ARPES_data - tutorial/3_metadata_collection_and_export_to_NeXus - tutorial/4_hextof_workflow.ipynb - tutorial/6_binning_with_time-stamped_data - tutorial/7_correcting_orthorhombic_symmetry - tutorial/8_jittering_tutorial - -.. toctree:: - :maxdepth: 1 - :caption: SED Core Modules - - sed/core - sed/dfops - sed/loader - sed/binning - sed/calibrator - sed/dataset - sed/diagnostic - sed/io - sed/metadata - sed/config - -.. toctree:: - :maxdepth: 2 - :caption: Contributing - - misc/contributing - misc/maintain - -Indices and tables -================== - -* :ref:`genindex` -* :ref:`modindex` -* :ref:`search` diff --git a/docs/misc/contributing.rst b/docs/misc/contributing.rst index ab12e517..b1938a20 100644 --- a/docs/misc/contributing.rst +++ b/docs/misc/contributing.rst @@ -8,7 +8,6 @@ Whether you are a beamline scientist hoping to create a loader for your data, or This guide will walk you through the process of setting up your development environment, and the workflow for contributing to the project. -.. contents:: Getting Started =============== @@ -73,7 +72,7 @@ Development Workflow 3. **Write Tests:** If your contribution introduces new features or fixes a bug, add tests to cover your changes. -4. **Run Tests:** To ensure no functionality is broken, run the tests: +4. **Run Tests:** To ensure no funtionality is broken, run the tests: .. code-block:: bash diff --git a/docs/misc/contribution.md b/docs/misc/contribution.md new file mode 100644 index 00000000..88d7b568 --- /dev/null +++ b/docs/misc/contribution.md @@ -0,0 +1,8 @@ +# Development + +```{toctree} +:maxdepth: 2 + +contributing +maintain +``` diff --git a/docs/misc/maintain.rst b/docs/misc/maintain.rst index 486f426a..6e887502 100644 --- a/docs/misc/maintain.rst +++ b/docs/misc/maintain.rst @@ -140,7 +140,7 @@ To create a release, follow these steps: c. **If you don't see update on PyPI:** - Visit the GitHub Actions page and monitor the Release workflow (https://github.com/OpenCOMPES/sed/actions/workflows/release.yml). - - Check if errors occurred. + - Check if errors occured. **Understanding the Release Workflow** diff --git a/docs/sed/api.rst b/docs/sed/api.rst new file mode 100644 index 00000000..fffcc53f --- /dev/null +++ b/docs/sed/api.rst @@ -0,0 +1,17 @@ +====== +API +====== + +.. toctree:: + :maxdepth: 1 + + core + dfops + loader + binning + calibrator + dataset + diagnostic + io + metadata + config diff --git a/docs/sed/config.rst b/docs/sed/config.rst index c5eac7a2..485bd7ea 100644 --- a/docs/sed/config.rst +++ b/docs/sed/config.rst @@ -1,17 +1,4 @@ Config -=================================================== -The config module contains a mechanics to collect configuration parameters from various sources and configuration files, and to combine them in a hierarchical manner into a single, consistent configuration dictionary. -It will load an (optional) provided config file, or alternatively use a passed python dictionary as initial config dictionary, and subsequently look for the following additional config files to load: - -* ``folder_config``: A config file of name :file:`sed_config.yaml` in the current working directory. This is mostly intended to pass calibration parameters of the workflow between different notebook instances. -* ``user_config``: A config file provided by the user, stored as :file:`.config/sed/config.yaml` in the current user's home directly. This is intended to give a user the option for individual configuration modifications of system settings. -* ``system_config``: A config file provided by the system administrator, stored as :file:`/etc/sed/config.yaml` on Linux-based systems, and :file:`%ALLUSERSPROFILE%/sed/config.yaml` on Windows. This should provide all necessary default parameters for using the sed processor with a given setup. For an example for an mpes setup, see :ref:`example_config` -* ``default_config``: The default configuration shipped with the package. Typically, all parameters here should be overwritten by any of the other configuration files. - -The config mechanism returns the combined dictionary, and reports the loaded configuration files. In order to disable or overwrite any of the configuration files, they can be also given as optional parameters (path to a file, or python dictionary). - - -API *************************************************** .. automodule:: sed.core.config :members: @@ -19,21 +6,3 @@ API .. _example_config: - -Default configuration settings -*************************************************** - -.. literalinclude:: ../../sed/config/default.yaml - :language: yaml - -Example configuration file for mpes (METIS momentum microscope at FHI-Berlin) -********************************************************************************* - -.. literalinclude:: ../../sed/config/mpes_example_config.yaml - :language: yaml - -Example configuration file for flash (HEXTOF momentum microscope at FLASH, Desy) -********************************************************************************* - -.. literalinclude:: ../../sed/config/flash_example_config.yaml - :language: yaml diff --git a/docs/sed/dataset.rst b/docs/sed/dataset.rst index 05bd94c0..6a8c57f8 100644 --- a/docs/sed/dataset.rst +++ b/docs/sed/dataset.rst @@ -64,7 +64,7 @@ Setting the “use_existing” keyword to False allows to download the data in a Interrupting extraction has similar behavior to download and just continues from where it stopped. '''''''''''''''''''''''''''''''''''''''''''''''''''''''''''''''''''''''''''''''''''''''''''''''''' -Or if user deletes the extracted documents, it re-extracts from zip file +Or if user deletes the extracted documents, it reextracts from zip file ''''''''''''''''''''''''''''''''''''''''''''''''''''''''''''''''''''''' .. code:: python diff --git a/docs/user_guide/config.md b/docs/user_guide/config.md new file mode 100644 index 00000000..581452d0 --- /dev/null +++ b/docs/user_guide/config.md @@ -0,0 +1,29 @@ +# Configuration + +The config module contains a mechanis to collect configuration parameters from various sources and configuration files, and to combine them in a hierachical manner into a single, consistent configuration dictionary. +It will load an (optional) provided config file, or alternatively use a passed python dictionary as initial config dictionary, and subsequently look for the following additional config files to load: + +* ``folder_config``: A config file of name :file:`sed_config.yaml` in the current working directory. This is mostly intended to pass calibration parameters of the workflow between different notebook instances. +* ``user_config``: A config file provided by the user, stored as :file:`.sed/config.yaml` in the current user's home directly. This is intended to give a user the option for individual configuration modifications of system settings. +* ``system_config``: A config file provided by the system administrator, stored as :file:`/etc/sed/config.yaml` on Linux-based systems, and :file:`%ALLUSERPROFILE%/sed/config.yaml` on Windows. This should provide all necessary default parameters for using the sed processor with a given setup. For an example for an mpes setup, see :ref:`example_config` +* ``default_config``: The default configuration shipped with the package. Typically, all parameters here should be overwritten by any of the other configuration files. + +The config mechanism returns the combined dictionary, and reports the loaded configuration files. In order to disable or overwrite any of the configuration files, they can be also given as optional parameters (path to a file, or python dictionary). + +## Default configuration settings + +```{literalinclude} ../../sed/config/default.yaml +:language: yaml +``` + +## Example configuration file for mpes (METIS momentum microscope at FHI-Berlin) + +```{literalinclude} ../../sed/config/mpes_example_config.yaml +:language: yaml +``` + +## Example configuration file for flash (HEXTOF momentum microscope at FLASH, Desy) + +```{literalinclude} ../../sed/config/flash_example_config.yaml +:language: yaml +``` diff --git a/docs/user_guide/index.md b/docs/user_guide/index.md new file mode 100644 index 00000000..489a30c6 --- /dev/null +++ b/docs/user_guide/index.md @@ -0,0 +1,25 @@ +--- +myst: + html_meta: + "description lang=en": | + Documentation for beginner users. +--- +# User Guide + +```{toctree} +:caption: Installing SED +:maxdepth: 1 +installation +``` + +```{toctree} +:caption: Basic concepts +../tutorial/1_binning_fake_data +../tutorial/8_jittering_tutorial +../tutorial/3_metadata_collection_and_export_to_NeXus +``` + +```{toctree} +:caption: Advance +config +``` diff --git a/docs/user_guide/installation.md b/docs/user_guide/installation.md new file mode 100644 index 00000000..8c3f44dd --- /dev/null +++ b/docs/user_guide/installation.md @@ -0,0 +1,74 @@ +# Installation + +```{attention} +Requires Python 3.9+ and pip installed. +``` + +- Create a new virtual environment using either venv, pyenv, conda, etc. See below for an example. + +```bash +python -m venv .sed-venv +``` + +- Activate your environment: + +```bash +# On macOS/Linux +source .sed-venv/bin/activate + +# On Windows +.sed-venv\Scripts\activate +``` + +- Install `sed`, distributed as `sed-processor` on PyPI: + +```bash +pip install sed-processor[all] +``` + +- If you do not use Jupyter Notebook or Jupyter Lab, you can skip the installing those dependencies: + +```bash +pip install sed-processor +``` + +```{note} +If you intend to work with Jupyter notebooks, it is helpful to install a Jupyter kernel for your environment. This can be done, once your environment is activated, by typing: +```bash +python -m ipykernel install --user --name=sed_kernel +``` + +# Development version + +```{attention} +Requires Git, Python 3.9+ and pip installed. +``` + +1. Clone the repository: + +```bash +git clone https://github.com/OpenCOMPES/sed.git +cd sed +``` + +2. Create and activate a virtual environment: + +```bash +# Create a virtual environment +python -m venv .sed-dev + +# Activate the virtual environment +# On macOS/Linux +source .sed-dev/bin/activate + +# On Windows +.sed-dev\Scripts\activate +``` + +3. Install the repository in editable mode with all dependencies: + +```bash +pip install -e .[all] +``` + +Now you have the development version of `sed` installed in your local environment. Feel free to make changes and submit pull requests. diff --git a/docs/workflows/index.md b/docs/workflows/index.md new file mode 100644 index 00000000..f3b15cff --- /dev/null +++ b/docs/workflows/index.md @@ -0,0 +1,15 @@ +--- +myst: + html_meta: + "description lang=en": | + Workflows showcasing different SED loaders and methods +--- +# Workflows + +```{toctree} +:caption: Basic concepts +../tutorial/2_conversion_pipeline_for_example_time-resolved_ARPES_data +../tutorial/4_hextof_workflow +../tutorial/6_binning_with_time-stamped_data +../tutorial/7_correcting_orthorhombic_symmetry +``` From 934dd1d1a8e9ec015c95aa26d83f9a3ecb792287 Mon Sep 17 00:00:00 2001 From: Zain Sohail Date: Mon, 15 Jul 2024 18:50:07 +0200 Subject: [PATCH 02/18] update yaml file for pushing to docs repo --- .github/workflows/documentation.yml | 83 +++++++++++++++++------------ 1 file changed, 49 insertions(+), 34 deletions(-) diff --git a/.github/workflows/documentation.yml b/.github/workflows/documentation.yml index 6c417d67..bc3467df 100644 --- a/.github/workflows/documentation.yml +++ b/.github/workflows/documentation.yml @@ -3,6 +3,7 @@ on: # Triggers the workflow on push but only for the main branch push: branches: [ main ] + tags: [ v* ] paths: - sed/**/* - tutorial/** @@ -11,18 +12,6 @@ on: 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 - jobs: build: runs-on: ubuntu-latest @@ -47,8 +36,8 @@ jobs: - name: "Setup Python, Poetry and Dependencies" uses: packetcoders/action-setup-cache-python-poetry@main with: - python-version: 3.8 - poetry-version: 1.2.2 + python-version: 3.9 + poetry-version: 1.8.3 - name: Install notebook dependencies run: poetry install -E notebook --with docs @@ -65,13 +54,6 @@ jobs: cp -r $GITHUB_WORKSPACE/sed/config $GITHUB_WORKSPACE/docs/sed rm $GITHUB_WORKSPACE/docs/tutorial/5_sxp_workflow.ipynb - # To be included later - # - name: Cache docs build - # id: cache-docs - # uses: actions/cache@v3 - # with: - # path: $GITHUB_WORKSPACE/_build - # key: ${{ runner.os }}-docs - name: download RAW data # if: steps.cache-primes.outputs.cache-hit != 'true' @@ -87,22 +69,55 @@ jobs: - name: build Sphinx docs run: poetry run sphinx-build -b html $GITHUB_WORKSPACE/docs $GITHUB_WORKSPACE/_build - - name: Setup Pages - uses: actions/configure-pages@v4 - - name: Upload artifact - uses: actions/upload-pages-artifact@v3 + 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@v4 + - name: Checkout docs repo + uses: actions/checkout@v2 + with: + repository: ${{ github.repository_owner }}/docs + token: ${{ secrets.GITHUB_TOKEN }} + path: 'docs-repo' + + - 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=sed/$VERSION" >> $GITHUB_OUTPUT + else + echo "folder=sed/latest" >> $GITHUB_OUTPUT + fi + + - name: Copy documentation to the right version folder + run: | + mkdir -p docs-repo/${{ steps.version-folder.outputs.folder }} + cp -r sphinx-docs/* docs-repo/${{ steps.version-folder.outputs.folder }} + + - 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 From b299f7c4486f87f6de0e5e46b397ffc2d3725f6f Mon Sep 17 00:00:00 2001 From: Zain Sohail Date: Mon, 15 Jul 2024 18:53:08 +0200 Subject: [PATCH 03/18] fix cspell --- docs/misc/contributing.rst | 2 +- docs/misc/maintain.rst | 2 +- docs/sed/dataset.rst | 2 +- docs/user_guide/config.md | 2 +- 4 files changed, 4 insertions(+), 4 deletions(-) diff --git a/docs/misc/contributing.rst b/docs/misc/contributing.rst index b1938a20..7aab314a 100644 --- a/docs/misc/contributing.rst +++ b/docs/misc/contributing.rst @@ -72,7 +72,7 @@ Development Workflow 3. **Write Tests:** If your contribution introduces new features or fixes a bug, add tests to cover your changes. -4. **Run Tests:** To ensure no funtionality is broken, run the tests: +4. **Run Tests:** To ensure no functionality is broken, run the tests: .. code-block:: bash diff --git a/docs/misc/maintain.rst b/docs/misc/maintain.rst index 6e887502..cf8d0a93 100644 --- a/docs/misc/maintain.rst +++ b/docs/misc/maintain.rst @@ -140,7 +140,7 @@ To create a release, follow these steps: c. **If you don't see update on PyPI:** - Visit the GitHub Actions page and monitor the Release workflow (https://github.com/OpenCOMPES/sed/actions/workflows/release.yml). - - Check if errors occured. + - Check if errors occurred during the release process. **Understanding the Release Workflow** diff --git a/docs/sed/dataset.rst b/docs/sed/dataset.rst index 6a8c57f8..05bd94c0 100644 --- a/docs/sed/dataset.rst +++ b/docs/sed/dataset.rst @@ -64,7 +64,7 @@ Setting the “use_existing” keyword to False allows to download the data in a Interrupting extraction has similar behavior to download and just continues from where it stopped. '''''''''''''''''''''''''''''''''''''''''''''''''''''''''''''''''''''''''''''''''''''''''''''''''' -Or if user deletes the extracted documents, it reextracts from zip file +Or if user deletes the extracted documents, it re-extracts from zip file ''''''''''''''''''''''''''''''''''''''''''''''''''''''''''''''''''''''' .. code:: python diff --git a/docs/user_guide/config.md b/docs/user_guide/config.md index 581452d0..612c287f 100644 --- a/docs/user_guide/config.md +++ b/docs/user_guide/config.md @@ -1,6 +1,6 @@ # Configuration -The config module contains a mechanis to collect configuration parameters from various sources and configuration files, and to combine them in a hierachical manner into a single, consistent configuration dictionary. +The config module contains a mechanism to collect configuration parameters from various sources and configuration files, and to combine them in a hierarchical manner into a single, consistent configuration dictionary. It will load an (optional) provided config file, or alternatively use a passed python dictionary as initial config dictionary, and subsequently look for the following additional config files to load: * ``folder_config``: A config file of name :file:`sed_config.yaml` in the current working directory. This is mostly intended to pass calibration parameters of the workflow between different notebook instances. From 699d82fe13a300f03aee82281fb54854a4f1499a Mon Sep 17 00:00:00 2001 From: Zain Sohail Date: Mon, 15 Jul 2024 22:37:36 +0200 Subject: [PATCH 04/18] try to install pydata theme in actions workflow --- .github/workflows/documentation.yml | 5 +++++ pyproject.toml | 1 - 2 files changed, 5 insertions(+), 1 deletion(-) diff --git a/.github/workflows/documentation.yml b/.github/workflows/documentation.yml index bc3467df..44d74bec 100644 --- a/.github/workflows/documentation.yml +++ b/.github/workflows/documentation.yml @@ -66,6 +66,11 @@ jobs: cd $GITHUB_WORKSPACE/docs poetry run python scripts/build_flash_parquets.py + # to be removed later. This theme doesn't support <3.9 python and our lock file contains 3.8 + - name: install pydata-sphinx-theme + run: | + poetry run pip install pydata-sphinx-theme + - name: build Sphinx docs run: poetry run sphinx-build -b html $GITHUB_WORKSPACE/docs $GITHUB_WORKSPACE/_build diff --git a/pyproject.toml b/pyproject.toml index f9fd5514..c9854e6e 100644 --- a/pyproject.toml +++ b/pyproject.toml @@ -67,7 +67,6 @@ optional = true [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" From d345739d7cc8a41ae602b7fe25bdfce4cb2f8415 Mon Sep 17 00:00:00 2001 From: Zain Sohail Date: Wed, 31 Jul 2024 20:42:48 +0200 Subject: [PATCH 05/18] minor suggested changes --- .cspell/custom-dictionary.txt | 2 ++ .gitignore | 2 +- docs/user_guide/config.md | 2 +- docs/workflows/index.md | 1 - 4 files changed, 4 insertions(+), 3 deletions(-) diff --git a/.cspell/custom-dictionary.txt b/.cspell/custom-dictionary.txt index 128efab7..76abda61 100644 --- a/.cspell/custom-dictionary.txt +++ b/.cspell/custom-dictionary.txt @@ -286,6 +286,7 @@ ptargs pullrequest pval pyarrow +pydata pyenv pygments pynxtools @@ -370,6 +371,7 @@ utime varnames venv verts +viewcode vmax voxels VTOF diff --git a/.gitignore b/.gitignore index 59fa215f..e7828d0f 100644 --- a/.gitignore +++ b/.gitignore @@ -5,7 +5,7 @@ *.hdf5 *.nxs *.nx -*.nxs +*.parquet *.zip **/datasets/* **/processed/* diff --git a/docs/user_guide/config.md b/docs/user_guide/config.md index 612c287f..7fb62f7d 100644 --- a/docs/user_guide/config.md +++ b/docs/user_guide/config.md @@ -5,7 +5,7 @@ It will load an (optional) provided config file, or alternatively use a passed p * ``folder_config``: A config file of name :file:`sed_config.yaml` in the current working directory. This is mostly intended to pass calibration parameters of the workflow between different notebook instances. * ``user_config``: A config file provided by the user, stored as :file:`.sed/config.yaml` in the current user's home directly. This is intended to give a user the option for individual configuration modifications of system settings. -* ``system_config``: A config file provided by the system administrator, stored as :file:`/etc/sed/config.yaml` on Linux-based systems, and :file:`%ALLUSERPROFILE%/sed/config.yaml` on Windows. This should provide all necessary default parameters for using the sed processor with a given setup. For an example for an mpes setup, see :ref:`example_config` +* ``system_config``: A config file provided by the system administrator, stored as :file:`/etc/sed/config.yaml` on Linux-based systems, and :file:`%ALLUSERSPROFILE%/sed/config.yaml` on Windows. This should provide all necessary default parameters for using the sed processor with a given setup. For an example for an mpes setup, see :ref:`example_config` * ``default_config``: The default configuration shipped with the package. Typically, all parameters here should be overwritten by any of the other configuration files. The config mechanism returns the combined dictionary, and reports the loaded configuration files. In order to disable or overwrite any of the configuration files, they can be also given as optional parameters (path to a file, or python dictionary). diff --git a/docs/workflows/index.md b/docs/workflows/index.md index f3b15cff..5b63b574 100644 --- a/docs/workflows/index.md +++ b/docs/workflows/index.md @@ -7,7 +7,6 @@ myst: # Workflows ```{toctree} -:caption: Basic concepts ../tutorial/2_conversion_pipeline_for_example_time-resolved_ARPES_data ../tutorial/4_hextof_workflow ../tutorial/6_binning_with_time-stamped_data From 540f4474b829cba25cb8b8c1354cc9b5766db946 Mon Sep 17 00:00:00 2001 From: rettigl Date: Tue, 22 Oct 2024 21:08:06 +0200 Subject: [PATCH 06/18] add suggested review changes --- .github/workflows/documentation.yml | 2 ++ docs/advanced_topics/index.md | 13 +++++++++++++ docs/index.md | 10 ++++++++++ docs/user_guide/index.md | 2 +- docs/workflows/index.md | 2 +- 5 files changed, 27 insertions(+), 2 deletions(-) create mode 100644 docs/advanced_topics/index.md diff --git a/.github/workflows/documentation.yml b/.github/workflows/documentation.yml index 44d74bec..a453e9a9 100644 --- a/.github/workflows/documentation.yml +++ b/.github/workflows/documentation.yml @@ -117,6 +117,8 @@ jobs: 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: | diff --git a/docs/advanced_topics/index.md b/docs/advanced_topics/index.md new file mode 100644 index 00000000..82a6d02c --- /dev/null +++ b/docs/advanced_topics/index.md @@ -0,0 +1,13 @@ +--- +myst: + html_meta: + "description lang=en": | + Advanced topics describing specific workflows and functionalities +--- +# Workflows + +```{toctree} +../tutorial/6_binning_with_time-stamped_data +../tutorial/7_correcting_orthorhombic_symmetry +../tutorial/8_jittering_tutorial +``` diff --git a/docs/index.md b/docs/index.md index 0f368f80..6b4cf732 100644 --- a/docs/index.md +++ b/docs/index.md @@ -30,6 +30,16 @@ Several example notebooks to demonstrate the functionality of SED for end-to-end workflows/index ``` +## Advanced topics + +There are also further example notebooks showing more advanced topics not required in every-day analysis. + +```{toctree} +:maxdepth: 2 + +advanced_topics/index +``` + ## API ```{toctree} diff --git a/docs/user_guide/index.md b/docs/user_guide/index.md index 489a30c6..504782d9 100644 --- a/docs/user_guide/index.md +++ b/docs/user_guide/index.md @@ -15,7 +15,7 @@ installation ```{toctree} :caption: Basic concepts ../tutorial/1_binning_fake_data -../tutorial/8_jittering_tutorial +../tutorial/2_conversion_pipeline_for_example_time-resolved_ARPES_data ../tutorial/3_metadata_collection_and_export_to_NeXus ``` diff --git a/docs/workflows/index.md b/docs/workflows/index.md index 5b63b574..eb2b6df7 100644 --- a/docs/workflows/index.md +++ b/docs/workflows/index.md @@ -7,8 +7,8 @@ myst: # Workflows ```{toctree} -../tutorial/2_conversion_pipeline_for_example_time-resolved_ARPES_data ../tutorial/4_hextof_workflow +../tutorial/8_jittering_tutorial ../tutorial/6_binning_with_time-stamped_data ../tutorial/7_correcting_orthorhombic_symmetry ``` From 71d53b12824d30a980542353e61f7af2867a1205 Mon Sep 17 00:00:00 2001 From: rettigl Date: Wed, 23 Oct 2024 11:13:29 +0200 Subject: [PATCH 07/18] update lockfile --- poetry.lock | 128 ++++++++++++++++++++++++++-------------------------- 1 file changed, 64 insertions(+), 64 deletions(-) diff --git a/poetry.lock b/poetry.lock index acf27ecf..fce9d4f1 100644 --- a/poetry.lock +++ b/poetry.lock @@ -1,4 +1,4 @@ -# This file is automatically @generated by Poetry 1.8.4 and should not be changed by hand. +# This file is automatically @generated by Poetry 1.8.3 and should not be changed by hand. 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-../tutorial/7_correcting_orthorhombic_symmetry ``` From b37674e85be1104c61f967bbc914e8a47b7a0710 Mon Sep 17 00:00:00 2001 From: rettigl Date: Wed, 23 Oct 2024 22:13:33 +0200 Subject: [PATCH 09/18] fix several docs issues --- docs/index.md | 16 +++------ docs/sed/dataset.rst | 36 ++++++------------- docs/sed/loader.rst | 1 + .../advanced_topics.md} | 9 +---- docs/user_guide/index.md | 9 +++-- tutorial/1_binning_fake_data.ipynb | 7 ++-- ...for_example_time-resolved_ARPES_data.ipynb | 12 +++++-- 7 files changed, 36 insertions(+), 54 deletions(-) rename docs/{advanced_topics/index.md => user_guide/advanced_topics.md} (50%) diff --git a/docs/index.md b/docs/index.md index 6b4cf732..1ba91d3c 100644 --- a/docs/index.md +++ b/docs/index.md @@ -13,8 +13,12 @@ SED (Single Event Data Frame) is a collection of routines and utilities to handl It features lazy evaluation of dataframe processing using dask, numba-accelerated multi-dimensional binning, calibration and correction for trARPES (Time- and angle-resolved photoemission spectroscopy) datasets. The package ensures provenance and FAIR data through metadata tracking, usage of the community defined NeXus format. +## User guide + +We introduce different functionalities of the package by several step-by-step use guides: + ```{toctree} -:maxdepth: 2 +:maxdepth: 1 user_guide/index @@ -30,16 +34,6 @@ Several example notebooks to demonstrate the functionality of SED for end-to-end workflows/index ``` -## Advanced topics - -There are also further example notebooks showing more advanced topics not required in every-day analysis. - -```{toctree} -:maxdepth: 2 - -advanced_topics/index -``` - ## API ```{toctree} diff --git a/docs/sed/dataset.rst b/docs/sed/dataset.rst index 05bd94c0..b0147464 100644 --- a/docs/sed/dataset.rst +++ b/docs/sed/dataset.rst @@ -13,14 +13,12 @@ Getting datasets import os from sed.dataset import dataset -Get -~~~ +get() +^^^^^ The “get” just needs the data name, but another root_dir can be provided. -^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^ Try to interrupt the download process and restart to see that it continues the download from where it stopped -''''''''''''''''''''''''''''''''''''''''''''''''''''''''''''''''''''''''''''''''''''''''''''''''''''''''''''' .. code:: python @@ -39,14 +37,12 @@ Try to interrupt the download process and restart to see that it continues the d Download complete. Not providing “remove_zip” at all will by default delete the zip file after extraction -'''''''''''''''''''''''''''''''''''''''''''''''''''''''''''''''''''''''''''''''''''''' .. code:: python dataset.get("WSe2") Setting the “use_existing” keyword to False allows to download the data in another location. Default is to use existing data -'''''''''''''''''''''''''''''''''''''''''''''''''''''''''''''''''''''''''''''''''''''''''''''''''''''''''''''''''''''''''''' .. code:: python @@ -62,10 +58,8 @@ Setting the “use_existing” keyword to False allows to download the data in a Interrupting extraction has similar behavior to download and just continues from where it stopped. -'''''''''''''''''''''''''''''''''''''''''''''''''''''''''''''''''''''''''''''''''''''''''''''''''' Or if user deletes the extracted documents, it re-extracts from zip file -''''''''''''''''''''''''''''''''''''''''''''''''''''''''''''''''''''''' .. code:: python @@ -90,11 +84,12 @@ Or if user deletes the extracted documents, it re-extracts from zip file WSe2 data extracted successfully. +remove() +^^^^^^^^ + “remove” allows removal of some or all instances of existing data -^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^ This would remove only one of the two existing paths -'''''''''''''''''''''''''''''''''''''''''''''''''''' .. code:: python @@ -105,7 +100,6 @@ This would remove only one of the two existing paths Removed /datasets/WSe2 This removes all instances, if any present -'''''''''''''''''''''''''''''''''''''''''' .. code:: python @@ -116,10 +110,9 @@ This removes all instances, if any present WSe2 data is not present. Attributes useful for user -~~~~~~~~~~~~~~~~~~~~~~~~~~ +^^^^^^^^^^^^^^^^^^^^^^^^^^ All available datasets after looking at module, user and folder levels -'''''''''''''''''''''''''''''''''''''''''''''''''''''''''''''''''''''' .. code:: python @@ -130,7 +123,6 @@ All available datasets after looking at module, user and folder levels ['WSe2', 'TaS2', 'Gd_W110'] The dir and subdirs where data is located -''''''''''''''''''''''''''''''''''''''''' .. code:: python @@ -150,7 +142,6 @@ The dir and subdirs where data is located '/datasets/WSe2/energycal_2019_01_08'] Existing locations where data is present -'''''''''''''''''''''''''''''''''''''''' .. code:: python @@ -164,11 +155,12 @@ Existing locations where data is present Example of adding custom datasets --------------------------------- +DatasetsManager +^^^^^^^^^^^^^^^ + Allows to add or remove datasets in json file at any level (module, user, folder). -'''''''''''''''''''''''''''''''''''''''''''''''''''''''''''''''''''''''''''''''''' Looks at all levels to give the available datasets -'''''''''''''''''''''''''''''''''''''''''''''''''' .. code:: python @@ -176,10 +168,8 @@ Looks at all levels to give the available datasets from sed.dataset import DatasetsManager We add a new dataset to both folder and user levels -''''''''''''''''''''''''''''''''''''''''''''''''''' This dataset also has “rearrange_files” set to True, which takes all files in subfolders and puts them in the main dataset specific directory -''''''''''''''''''''''''''''''''''''''''''''''''''''''''''''''''''''''''''''''''''''''''''''''''''''''''''''''''''''''''''''''''''''''''''''' .. code:: python @@ -198,7 +188,6 @@ This dataset also has “rearrange_files” set to True, which takes all files i Added Example dataset to user datasets.json datasets.json should be available in execution folder after this -'''''''''''''''''''''''''''''''''''''''''''''''''''''''''''''''' .. code:: python @@ -210,7 +199,6 @@ datasets.json should be available in execution folder after this ['Example', 'WSe2', 'TaS2', 'Gd_W110'] This will remove the Example dataset from the user json file -'''''''''''''''''''''''''''''''''''''''''''''''''''''''''''' .. code:: python @@ -221,7 +209,6 @@ This will remove the Example dataset from the user json file Removed Example dataset from user datasets.json Adding dataset that already exists will give an error. Likewise, removing one that doesn’t exist -'''''''''''''''''''''''''''''''''''''''''''''''''''''''''''''''''''''''''''''''''''''''''''''''' .. code:: python @@ -234,7 +221,6 @@ Adding dataset that already exists will give an error. Likewise, removing one th Now that dataset.json with Example exists in current dir, lets try to fetch it -'''''''''''''''''''''''''''''''''''''''''''''''''''''''''''''''''''''''''''''' .. code:: python @@ -272,7 +258,6 @@ Now that dataset.json with Example exists in current dir, lets try to fetch it [] lets download to another location -''''''''''''''''''''''''''''''''' .. code:: python @@ -300,7 +285,6 @@ lets download to another location Rearranging complete. we can remove one instance -'''''''''''''''''''''''''' .. code:: python @@ -332,7 +316,7 @@ we can remove one instance ['/datasets/Example'] Default datasets.json ------------------------- +--------------------- .. literalinclude:: ../../sed/dataset/datasets.json :language: json diff --git a/docs/sed/loader.rst b/docs/sed/loader.rst index 87fdebdb..468f34e4 100644 --- a/docs/sed/loader.rst +++ b/docs/sed/loader.rst @@ -10,6 +10,7 @@ Loader Interface :undoc-members: .. _base_loader: + Abstract BaseLoader ################################################### .. automodule:: sed.loader.base.loader diff --git a/docs/advanced_topics/index.md b/docs/user_guide/advanced_topics.md similarity index 50% rename from docs/advanced_topics/index.md rename to docs/user_guide/advanced_topics.md index 82a6d02c..ebd773c8 100644 --- a/docs/advanced_topics/index.md +++ b/docs/user_guide/advanced_topics.md @@ -1,12 +1,5 @@ ---- -myst: - html_meta: - "description lang=en": | - Advanced topics describing specific workflows and functionalities ---- -# Workflows - ```{toctree} +:maxdepth: 1 ../tutorial/6_binning_with_time-stamped_data ../tutorial/7_correcting_orthorhombic_symmetry ../tutorial/8_jittering_tutorial diff --git a/docs/user_guide/index.md b/docs/user_guide/index.md index 504782d9..e7b4e90a 100644 --- a/docs/user_guide/index.md +++ b/docs/user_guide/index.md @@ -2,7 +2,7 @@ myst: html_meta: "description lang=en": | - Documentation for beginner users. + Documentation for users. --- # User Guide @@ -14,12 +14,15 @@ installation ```{toctree} :caption: Basic concepts +:maxdepth: 1 ../tutorial/1_binning_fake_data ../tutorial/2_conversion_pipeline_for_example_time-resolved_ARPES_data ../tutorial/3_metadata_collection_and_export_to_NeXus +config ``` ```{toctree} -:caption: Advance -config +:maxdepth: 1 +:caption: Advanced Topics +advanced_topics ``` diff --git a/tutorial/1_binning_fake_data.ipynb b/tutorial/1_binning_fake_data.ipynb index 04370e8e..01e987ae 100644 --- a/tutorial/1_binning_fake_data.ipynb +++ b/tutorial/1_binning_fake_data.ipynb @@ -20,8 +20,6 @@ "metadata": {}, "outputs": [], "source": [ - "import sys\n", - "\n", "import dask\n", "import numpy as np\n", "import pandas as pd\n", @@ -29,8 +27,9 @@ "\n", "import matplotlib.pyplot as plt\n", "\n", - "sys.path.append(\"../\")\n", - "from sed.binning import bin_partition, bin_dataframe" + "from sed.binning import bin_partition, bin_dataframe\n", + "\n", + "%matplotlib widget" ] }, { diff --git a/tutorial/2_conversion_pipeline_for_example_time-resolved_ARPES_data.ipynb b/tutorial/2_conversion_pipeline_for_example_time-resolved_ARPES_data.ipynb index 7b9cb1e2..6ee3d7c1 100644 --- a/tutorial/2_conversion_pipeline_for_example_time-resolved_ARPES_data.ipynb +++ b/tutorial/2_conversion_pipeline_for_example_time-resolved_ARPES_data.ipynb @@ -315,13 +315,21 @@ "sp.apply_momentum_calibration()" ] }, + { + "cell_type": "markdown", + "id": "74e7ef75", + "metadata": {}, + "source": [ + "## Energy Correction and Calibration workflow" + ] + }, { "attachments": {}, "cell_type": "markdown", "id": "0bce2388", "metadata": {}, "source": [ - "## Energy Correction (optional)\n", + "### Energy Correction (optional)\n", "The purpose of the energy correction is to correct for any momentum-dependent distortion of the energy axis, e.g. from geometric effects in the flight tube, or from space charge" ] }, @@ -394,7 +402,7 @@ "id": "8b571b4c", "metadata": {}, "source": [ - "## 3. Energy calibration\n", + "### Energy calibration\n", "For calibrating the energy axis, a set of data taken at different bias voltages around the value where the measurement was taken is required." ] }, From bf8d7bdcc418676f9b24804a7118f6118054f041 Mon Sep 17 00:00:00 2001 From: rettigl Date: Wed, 23 Oct 2024 22:31:32 +0200 Subject: [PATCH 10/18] test creation of develop version docs --- .github/workflows/documentation.yml | 4 +++- 1 file changed, 3 insertions(+), 1 deletion(-) diff --git a/.github/workflows/documentation.yml b/.github/workflows/documentation.yml index a453e9a9..06558221 100644 --- a/.github/workflows/documentation.yml +++ b/.github/workflows/documentation.yml @@ -109,8 +109,10 @@ jobs: if [[ $GITHUB_REF == refs/tags/* ]]; then VERSION=${GITHUB_REF#refs/tags/} echo "folder=sed/$VERSION" >> $GITHUB_OUTPUT - else + elif [[ $GITHUB_REF == refs/heads/main ]]; then echo "folder=sed/latest" >> $GITHUB_OUTPUT + else + echo "folder=sed/develop" >> $GITHUB_OUTPUT fi - name: Copy documentation to the right version folder From 8e97db24b5592b15b673fd9e36535325b54bc90f Mon Sep 17 00:00:00 2001 From: rettigl Date: Thu, 24 Oct 2024 21:45:10 +0200 Subject: [PATCH 11/18] add script for updating switcher.json --- .github/workflows/documentation.yml | 5 +++++ 1 file changed, 5 insertions(+) diff --git a/.github/workflows/documentation.yml b/.github/workflows/documentation.yml index 06558221..0ce4f59f 100644 --- a/.github/workflows/documentation.yml +++ b/.github/workflows/documentation.yml @@ -115,6 +115,11 @@ jobs: echo "folder=sed/develop" >> $GITHUB_OUTPUT fi + - name: Update switcher.json + run: | + echo "poetry run python docs-repo/sed/update_switcher.py docs-repo/sed/switcher.json $GITHUB_REF" + poetry run python docs-repo/sed/update_switcher.py docs-repo/sed/switcher.json $GITHUB_REF + - name: Copy documentation to the right version folder run: | mkdir -p docs-repo/${{ steps.version-folder.outputs.folder }} From a40a479de637d757b0489b1f47de3dc3bf26e34b Mon Sep 17 00:00:00 2001 From: rettigl Date: Thu, 24 Oct 2024 22:49:49 +0200 Subject: [PATCH 12/18] install python for updating switcher file --- .github/workflows/documentation.yml | 9 +++++++-- docs/index.md | 2 +- 2 files changed, 8 insertions(+), 3 deletions(-) diff --git a/.github/workflows/documentation.yml b/.github/workflows/documentation.yml index 0ce4f59f..3dfa4da9 100644 --- a/.github/workflows/documentation.yml +++ b/.github/workflows/documentation.yml @@ -92,6 +92,11 @@ jobs: token: ${{ secrets.GITHUB_TOKEN }} path: 'docs-repo' + - name: Set up Python 3.9 + uses: actions/setup-python@v4 + with: + python-version: 3.9 + - name: Setup SSH uses: webfactory/ssh-agent@v0.9.0 with: @@ -117,8 +122,8 @@ jobs: - name: Update switcher.json run: | - echo "poetry run python docs-repo/sed/update_switcher.py docs-repo/sed/switcher.json $GITHUB_REF" - poetry run python docs-repo/sed/update_switcher.py docs-repo/sed/switcher.json $GITHUB_REF + echo "python docs-repo/sed/update_switcher.py docs-repo/sed/switcher.json $GITHUB_REF" + python docs-repo/sed/update_switcher.py docs-repo/sed/switcher.json $GITHUB_REF - name: Copy documentation to the right version folder run: | diff --git a/docs/index.md b/docs/index.md index 1ba91d3c..afeefb05 100644 --- a/docs/index.md +++ b/docs/index.md @@ -18,7 +18,7 @@ The package ensures provenance and FAIR data through metadata tracking, usage of We introduce different functionalities of the package by several step-by-step use guides: ```{toctree} -:maxdepth: 1 +:maxdepth: 2 user_guide/index From 4fa525f7924b094e8afdf4b6bb2dcc4c0a361fff Mon Sep 17 00:00:00 2001 From: rettigl Date: Fri, 25 Oct 2024 10:50:10 +0200 Subject: [PATCH 13/18] fix user guide toctree, and use build version in switcher script --- .github/workflows/documentation.yml | 5 +++-- docs/user_guide/index.md | 7 ++++--- 2 files changed, 7 insertions(+), 5 deletions(-) diff --git a/.github/workflows/documentation.yml b/.github/workflows/documentation.yml index 3dfa4da9..0f338625 100644 --- a/.github/workflows/documentation.yml +++ b/.github/workflows/documentation.yml @@ -122,8 +122,9 @@ jobs: - name: Update switcher.json run: | - echo "python docs-repo/sed/update_switcher.py docs-repo/sed/switcher.json $GITHUB_REF" - python docs-repo/sed/update_switcher.py docs-repo/sed/switcher.json $GITHUB_REF + VERSION=`grep "SED documentation." index.html | sed -n 's/.*SED \(.*\) documentation.*/\1/p'` + echo "python docs-repo/sed/update_switcher.py docs-repo/sed/switcher.json $GITHUB_REF $VERSION" + python docs-repo/sed/update_switcher.py docs-repo/sed/switcher.json $GITHUB_REF $VERSION - name: Copy documentation to the right version folder run: | diff --git a/docs/user_guide/index.md b/docs/user_guide/index.md index e7b4e90a..16d36aaf 100644 --- a/docs/user_guide/index.md +++ b/docs/user_guide/index.md @@ -6,14 +6,14 @@ myst: --- # User Guide +## Installing SED ```{toctree} -:caption: Installing SED :maxdepth: 1 installation ``` +## Basic concepts ```{toctree} -:caption: Basic concepts :maxdepth: 1 ../tutorial/1_binning_fake_data ../tutorial/2_conversion_pipeline_for_example_time-resolved_ARPES_data @@ -21,8 +21,9 @@ installation config ``` +## Advanced Topics + ```{toctree} :maxdepth: 1 -:caption: Advanced Topics advanced_topics ``` From e8479576dff093d5c5d9f3e946936af546b0c3ea Mon Sep 17 00:00:00 2001 From: rettigl <l.rettig@web.de> Date: Fri, 25 Oct 2024 11:24:00 +0200 Subject: [PATCH 14/18] update readme.md --- README.md | 98 ++++++++++++++----------------------------------------- 1 file changed, 25 insertions(+), 73 deletions(-) diff --git a/README.md b/README.md index 848a5405..abc9a476 100644 --- a/README.md +++ b/README.md @@ -7,23 +7,21 @@ [![](https://img.shields.io/pypi/v/sed-processor)](https://pypi.org/project/sed-processor) [![Coverage Status](https://coveralls.io/repos/github/OpenCOMPES/sed/badge.svg?branch=main&kill_cache=1)](https://coveralls.io/github/OpenCOMPES/sed?branch=main) -Backend to handle photoelectron resolved datastreams. +**sed-processor** is a backend to process and bin multidimensional single-event datastreams, with the intended primary use case in multidimensional photoelectron spectroscopy using time-of-flight instruments. -# Table of Contents -[Installation](#installation) - - [For Users (pip)](#for-users-pip) - - [For Contributors (pip)](#for-contributors-pip) - - [For Maintainers (poetry)](#for-maintainers-poetry) +It builds on [Dask](https://www.dask.org/) dataframes, where each column represents a multidimensional "coordinate" such as position, time-of-flight, pump-probe delay etc, and each entry represents one electron. The `SedProcessor` class provides a single user entry point, and provides functions for handling various workflows for coordinate transformation, e.g. corrections and calibrations. -# Installation +Furthermore, "sed-processor" provides fast and parallelized binning routines to compute multidimensional histograms from the processed dataframes in a delayed fashion, thus reducing requirements on cpu power and memory consumption. + +Finally, in contains several export routines, including export into the [NeXus](https://www.nexusformat.org/) format with rich and standardized metadata annotation. -## For Users (pip) +# Installation -### Prerequisites +## Prerequisites - Python 3.8+ - pip -### Steps +## Steps - Create a new virtual environment using either venv, pyenv, conda, etc. See below for an example. ```bash @@ -58,75 +56,29 @@ python -m ipykernel install --user --name=sed_kernel pip install sed-processor ``` -## For Contributors (pip) - -### Prerequisites -- Git -- Python 3.8+ -- pip - -### Steps -1. Clone the repository: - -```bash -git clone https://github.com/OpenCOMPES/sed.git -cd sed -``` - -2. Create and activate a virtual environment: - -```bash -# Create a virtual environment -python -m venv .sed-dev +# Documentation +Comprehensive documentation including several workflow examples can be found here: +https://opencompes.github.io/docs/sed/latest/ -# Activate the virtual environment -# On macOS/Linux -source .sed-dev/bin/activate -# On Windows -.sed-dev\Scripts\activate -``` +# Contributing +Users are welcome to contribute to the development of **sed-processor**. Information how to contribute, including how to install developer versions can be found in the [documentation](https://opencompes.github.io/docs/sed/latest/misc/contribution.html) -3. Install the repository in editable mode with all dependencies: - -```bash -pip install -e .[all] -``` - -Now you have the development version of `sed` installed in your local environment. Feel free to make changes and submit pull requests. - -## For Maintainers (poetry) - -### Prerequisites -- Poetry: [Poetry Installation](https://python-poetry.org/docs/#installation) - -### Steps -- Create a virtual environment by typing: - -```bash -poetry shell -``` - -- A new shell will be spawned with the new environment activated. - -- Install the dependencies from the `pyproject.toml` by typing: - -```bash -poetry install --with dev, docs -``` +We would like to thank our contributors! -- If you wish to use the virtual environment created by Poetry to work in a Jupyter notebook, you first need to install the optional notebook dependencies and then create a Jupyter kernel for that. +[![Contributors](https://contrib.rocks/image?repo=OpenCOMPES/sed)](https://github.com/OpenCOMPES/sed/graphs/contributors) - - Install the optional dependencies: - ```bash - poetry install -E notebook - ``` +## License - - Make sure to run the command below within your virtual environment (`poetry run` ensures this) by typing: +sed-processor is licenced under the MIT license - ```bash - poetry run ipython kernel install --user --name=sed_poetry - ``` +Copyright (c) 2022-2024 OpenCOMPES - - The new kernel will now be available in your Jupyter kernels list. +THE SOFTWARE IS PROVIDED "AS IS", WITHOUT WARRANTY OF ANY KIND, EXPRESS OR +IMPLIED, INCLUDING BUT NOT LIMITED TO THE WARRANTIES OF MERCHANTABILITY, +FITNESS FOR A PARTICULAR PURPOSE AND NONINFRINGEMENT. IN NO EVENT SHALL THE +AUTHORS OR COPYRIGHT HOLDERS BE LIABLE FOR ANY CLAIM, DAMAGES OR OTHER +LIABILITY, WHETHER IN AN ACTION OF CONTRACT, TORT OR OTHERWISE, ARISING FROM, +OUT OF OR IN CONNECTION WITH THE SOFTWARE OR THE USE OR OTHER DEALINGS IN THE +SOFTWARE. From 514f555d1e24f1555272610c8f5e728045f7cb26 Mon Sep 17 00:00:00 2001 From: rettigl <l.rettig@web.de> Date: Fri, 25 Oct 2024 13:24:36 +0200 Subject: [PATCH 15/18] fix version determination, and add link to stable version --- .github/workflows/documentation.yml | 4 +++- 1 file changed, 3 insertions(+), 1 deletion(-) diff --git a/.github/workflows/documentation.yml b/.github/workflows/documentation.yml index 0f338625..fa1ca8f1 100644 --- a/.github/workflows/documentation.yml +++ b/.github/workflows/documentation.yml @@ -114,6 +114,8 @@ jobs: if [[ $GITHUB_REF == refs/tags/* ]]; then VERSION=${GITHUB_REF#refs/tags/} echo "folder=sed/$VERSION" >> $GITHUB_OUTPUT + rm docs-repo/sed/stable + ln -s -r docs-repo/sed/$VERSION docs-repo/sed/stable elif [[ $GITHUB_REF == refs/heads/main ]]; then echo "folder=sed/latest" >> $GITHUB_OUTPUT else @@ -122,7 +124,7 @@ jobs: - name: Update switcher.json run: | - VERSION=`grep "<title>SED documentation." index.html | sed -n 's/.*SED \(.*\) documentation.*/\1/p'` + VERSION=`grep "<title>SED documentation." sphinx-docs/index.html | sed -n 's/.*SED \(.*\) documentation.*/\1/p'` echo "python docs-repo/sed/update_switcher.py docs-repo/sed/switcher.json $GITHUB_REF $VERSION" python docs-repo/sed/update_switcher.py docs-repo/sed/switcher.json $GITHUB_REF $VERSION From 9718082824d79f00098e9835c793adead17316f0 Mon Sep 17 00:00:00 2001 From: rettigl <l.rettig@web.de> Date: Fri, 25 Oct 2024 15:18:10 +0200 Subject: [PATCH 16/18] rewrite version for develop builds --- .github/workflows/documentation.yml | 8 ++++++++ 1 file changed, 8 insertions(+) diff --git a/.github/workflows/documentation.yml b/.github/workflows/documentation.yml index fa1ca8f1..8a7124ca 100644 --- a/.github/workflows/documentation.yml +++ b/.github/workflows/documentation.yml @@ -71,6 +71,14 @@ jobs: run: | poetry run pip install pydata-sphinx-theme + - name: Change version for develop build + if: startsWith(github.ref, 'refs/heads/') && github.ref != 'refs/heads/main' + run: | + VERSION=`sed -n 's/^version = "\(.*\)".*/\1/p' $GITHUB_WORKSPACE/pyproject.toml` + MOD_VERSION=$VERSION".dev0" + echo $MOD_VERSION + sed -i "s/^version = \"$VERSION\"/version = \"$MOD_VERSION\"/" $GITHUB_WORKSPACE/pyproject.toml + - name: build Sphinx docs run: poetry run sphinx-build -b html $GITHUB_WORKSPACE/docs $GITHUB_WORKSPACE/_build From 544fce1c90bb672f00c7bfee4e5e0d4304e36d5e Mon Sep 17 00:00:00 2001 From: rettigl <l.rettig@web.de> Date: Fri, 25 Oct 2024 16:49:26 +0200 Subject: [PATCH 17/18] fix typo --- README.md | 2 +- 1 file changed, 1 insertion(+), 1 deletion(-) diff --git a/README.md b/README.md index abc9a476..1ff96bb7 100644 --- a/README.md +++ b/README.md @@ -9,7 +9,7 @@ **sed-processor** is a backend to process and bin multidimensional single-event datastreams, with the intended primary use case in multidimensional photoelectron spectroscopy using time-of-flight instruments. -It builds on [Dask](https://www.dask.org/) dataframes, where each column represents a multidimensional "coordinate" such as position, time-of-flight, pump-probe delay etc, and each entry represents one electron. The `SedProcessor` class provides a single user entry point, and provides functions for handling various workflows for coordinate transformation, e.g. corrections and calibrations. +It builds on [Dask](https://www.dask.org/) dataframes, where each column represents a multidimensional "coordinate" such as position, time-of-flight, pump-probe delay etc., and each entry represents one electron. The `SedProcessor` class provides a single user entry point, and provides functions for handling various workflows for coordinate transformation, e.g. corrections and calibrations. Furthermore, "sed-processor" provides fast and parallelized binning routines to compute multidimensional histograms from the processed dataframes in a delayed fashion, thus reducing requirements on cpu power and memory consumption. 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