diff --git a/.github/workflows/build.yml b/.github/workflows/build.yml index 0b1171db7..278104d73 100644 --- a/.github/workflows/build.yml +++ b/.github/workflows/build.yml @@ -21,9 +21,9 @@ jobs: python --version pip --version - - name: Install pypa/build + - name: Install pypa/build pypa/twine run: | - pip install build + pip install build twine - name: Build a binary wheel and a source tarball run: | @@ -32,6 +32,10 @@ jobs: - name: Display content dist folder run: | ls -l dist/ + + - name: Run twin check + run: | + twine check dist/* - uses: actions/upload-artifact@v3 with: diff --git a/.github/workflows/docs.yml b/.github/workflows/docs.yml new file mode 100644 index 000000000..0c64df58e --- /dev/null +++ b/.github/workflows/docs.yml @@ -0,0 +1,97 @@ +name: Docs + +on: [push, pull_request] + +jobs: + build_docs: + # This build is to make PR comments for the sphinx warning and check if + # web links are not broken + name: Check links and make PR comments + runs-on: ubuntu-latest + env: + DOCS_PATH: ./doc/_build/html/ + steps: + - uses: actions/checkout@v4 + with: + fetch-depth: 0 + + - uses: actions/setup-python@v4 + name: Install Python + with: + python-version: '3.11' + + - name: Install build docs + shell: bash -l {0} + run: | + pip install .'[doc]' + + # Add sphinx warnings as PR comments + - uses: sphinx-doc/sphinx-problem-matcher@master + + - name: Build docs + shell: bash -l {0} + run: | + cd doc + make SPHINXOPTS="-W --keep-going" html + + - uses: actions/upload-artifact@v3 + with: + path: ${{ env.DOCS_PATH }} + name: docs_html + + - name: Check links + shell: bash -l {0} + run: | + cd doc + make linkcheck + + push_docs: + # This build is to push changes to gh-pages branch (https://hyperspy.org/exspy) + needs: build_docs + name: Push to gh-pages + runs-on: ubuntu-latest + if: ${{ github.event_name != 'pull_request' && github.repository == 'hyperspy/exspy' }} + permissions: + # needs write permission to push the docs to gh-pages + contents: write + steps: + - uses: actions/checkout@v4 + with: + fetch-depth: 0 + ref: gh-pages + + - uses: actions/download-artifact@v3 + with: + name: docs_html + path: . + + - name: list files + run: | + ls + + - name: Git status + run: | + git status + git status -s + if [[ $(git status -s) ]]; then + HAS_CHANGES='true' + else + HAS_CHANGES='false' + fi + echo "HAS_CHANGES=${HAS_CHANGES}" >> $GITHUB_ENV + + - name: Commit files + # Skip when there is nothing to commit + if: ${{ env.HAS_CHANGES == 'true' }} + run: | + git config --local user.email "github-actions[bot]@users.noreply.github.com" + git config --local user.name "github-actions[bot]" + git add -A + git commit -m "Update docs build" -a + + - name: Push changes + if: ${{ env.HAS_CHANGES == 'true' }} + uses: ad-m/github-push-action@d91a481090679876dfc4178fef17f286781251df + with: + github_token: ${{ secrets.GITHUB_TOKEN }} + branch: gh-pages diff --git a/.github/workflows/tests.yml b/.github/workflows/tests.yml index 5f5f49217..6f1e9ba53 100644 --- a/.github/workflows/tests.yml +++ b/.github/workflows/tests.yml @@ -45,7 +45,7 @@ jobs: - name: Run test suite run: | - pytest --pyargs exspy + pytest --pyargs exspy -n 2 - name: Upload coverage to Codecov if: ${{ always() }} diff --git a/.gitignore b/.gitignore new file mode 100644 index 000000000..4f21eef4b --- /dev/null +++ b/.gitignore @@ -0,0 +1,5 @@ +doc/_build/* +doc/auto_examples/* +build/* +dist/* +*egg-info* \ No newline at end of file diff --git a/.readthedocs.yaml b/.readthedocs.yaml new file mode 100644 index 000000000..015d38882 --- /dev/null +++ b/.readthedocs.yaml @@ -0,0 +1,27 @@ +# .readthedocs.yml +# Read the Docs configuration file +# See https://docs.readthedocs.io/en/stable/config-file/v2.html for details + +# Required +version: 2 + +# Set the version of Python and other tools you might need +build: + os: ubuntu-22.04 + tools: + python: "3.11" + +# Build documentation in the docs/ directory with Sphinx +sphinx: + configuration: doc/conf.py + +# Optionally build your docs in additional formats such as PDF and ePub +formats: + - htmlzip + +python: + install: + - method: pip + path: . + extra_requirements: + - doc diff --git a/README.md b/README.md new file mode 100644 index 000000000..fb891cf77 --- /dev/null +++ b/README.md @@ -0,0 +1,14 @@ + +**exSpy** is a Python package extending the functionality for multi-dimensional +data analysis provided by the [HyperSpy](https://hyperspy.org) library. It is +aimed at helping with the analysis of X-rays Energy Dispersive Spectroscopy (EDS) +and Electron Energy Loss Spectroscopy (EELS). + +Go to the documentation for instructions on how to install exSpy and start an +analysis: [Read the docs](https://exspy.readthedocs.io). + +Everyone is welcome to contribute. Please read our +[contributing guidelines](https://github.com/hyperspy/exspy/blob/main/CONTRIBUTING.rst) and get started! + +Development of exSpy is documented in the +[changelog](https://github.com/hyperspy/exspy/blob/main/CHANGES.rst). diff --git a/README.rst b/README.rst deleted file mode 100644 index e69de29bb..000000000 diff --git a/doc/citing.rst b/doc/citing.rst index 95a22b02f..abb8985c7 100644 --- a/doc/citing.rst +++ b/doc/citing.rst @@ -6,7 +6,7 @@ Citing exSpy If exSpy has been significant to a project that leads to an academic publication, please acknowledge that fact by citing it. The DOI in the -badge below is the `Concept DOI `_ -- +badge below is the `Concept DOI `_ -- it can be used to cite the project without referring to a specific version. If you are citing HoloSpy because you have used it to process data, please use the DOI of the specific version that you have employed. You can diff --git a/doc/conf.py b/doc/conf.py index 6305cbfc1..7c4ea7c78 100644 --- a/doc/conf.py +++ b/doc/conf.py @@ -35,11 +35,24 @@ # "numpydoc", "sphinx_design", "sphinx_favicon", + "sphinx_copybutton", "sphinx.ext.autodoc", "sphinx.ext.autosummary", "sphinx.ext.githubpages", "sphinx.ext.intersphinx", "sphinx.ext.napoleon", + "sphinx_gallery.gen_gallery", +] + +linkcheck_ignore = [ + "https://doi.org/10.1021/acs.nanolett.5b00449", # 403 Client Error: Forbidden for url + "https://onlinelibrary.wiley.com/doi/10.1111/j.1365-2818.2006.01549.x", # 403 Client Error: Forbidden for url + # Remove when setup + "https://github.com/hyperspy/exspy-demos", + "https://www.anaconda.com/blog/understanding-conda-and-pip", # Transcient? + # Remove once it is merged and the links are working + "https://exspy.readthedocs.io", + "https://github.com/hyperspy/exspy/blob/main/releasing_guide.md", ] intersphinx_mapping = { @@ -87,6 +100,7 @@ "text": "exSpy", }, "header_links_before_dropdown": 6, + "navigation_with_keys": False, } # The name of an image file (relative to this directory) to place at the top @@ -119,5 +133,17 @@ } toc_object_entries_show_parents = "hide" -# def setup(app): -# app.add_css_file("custom-styles.css") +# -- Sphinx-Gallery--------------- + +# https://sphinx-gallery.github.io +sphinx_gallery_conf = { + "examples_dirs": "../examples", # path to your example scripts + "gallery_dirs": "auto_examples", # path to where to save gallery generated output + "filename_pattern": ".py", # pattern to define which will be executed + "ignore_pattern": "_sgskip.py", # pattern to define which will not be executed +} + +# -- Sphinx-copybutton ----------- + +copybutton_prompt_text = r">>> |\.\.\. " +copybutton_prompt_is_regexp = True diff --git a/doc/index.rst b/doc/index.rst index b3046771e..55eb1edf9 100644 --- a/doc/index.rst +++ b/doc/index.rst @@ -1,29 +1,12 @@ -Welcome to exSpy's documentation! -*********************************** -**exSpy** is a Python package extending the functionality for multi-dimensional -data analysis provided by the `HyperSpy `_ library. It is -aimed at helping with the analysis of X-rays Energy Dispersive Spectroscopy (EDS) -and Electron Energy Loss Spectroscopy (EELS). - -Check out the :ref:`installation ` section for further information, including -how to start using this project. - -.. note:: - - This is an open-source community project: everyone is welcome to contribute. - Please read our (see :ref:`contributing_label`) guidelines and get started! - -Contents -======== - .. toctree:: - :maxdepth: 2 - - user_guide/index.rst - reference/index.rst - changes.rst - Citing - contributing.rst - license.rst + :maxdepth: 1 + :hidden: + + User Guide + Examples + Reference + Release Notes + Citing + Contribute .. include:: intro.rst diff --git a/doc/intro.rst b/doc/intro.rst index 9e7a89173..2cefe5299 100644 --- a/doc/intro.rst +++ b/doc/intro.rst @@ -1,12 +1,18 @@ +Welcome to exSpy's documentation! +*********************************** +**exSpy** is a Python package extending the functionality for multi-dimensional +data analysis provided by the `HyperSpy `_ library. It is +aimed at helping with the analysis of X-rays Energy Dispersive Spectroscopy (EDS) +and Electron Energy Loss Spectroscopy (EELS). -What is exSpy -============= +Check out the :ref:`installation ` section for further information, +including how to start using this project. -exSpy is an open source Python library which provides tools to facilitate -the visualization and processing of EELS EDS and other spectroscopic data. +.. note:: + + This is an open-source community project: everyone is welcome to contribute. + Please read our (see :ref:`contributing_label`) guidelines and get started! -exSpy is built on top of HyperSpy, a Python library for multi-dimensional -data analysis and extends it with tools for the analysis of spectroscopic data. Learning resources ================== @@ -73,11 +79,11 @@ Learning resources There are many ways you can help! Citing exSpy -================= +============ If exSpy has been significant to a project that leads to an academic publication, please acknowledge that fact by citing it. The DOI in the -badge below is the `Concept DOI `_ of +badge below is the `Concept DOI `_ of HyperSpy. It can be used to cite the project without referring to a specific version. If you are citing exSpy because you have used it to process data, please use the DOI of the specific version that you have employed. You can @@ -98,7 +104,18 @@ HyperSpy in a scientific database e.g. `Google Scholar Articles published before 2012 may mention the HyperSpy project under its old name, `EELSLab`. -Credits + +License ======= -.. include:: ../AUTHORS.txt +**exSpy** is free software: you can redistribute it and/or modify +it under the terms of the `GNU General Public License (GPL) +`_ as published by +the Free Software Foundation, either version 3 of the license, or +(at your option) any later version. + +**exSpy** is distributed in the hope that it will be useful, +but **without any warranty**; without even the implied warranty of +**merchantability** or **fitness for a particular purpose**. See the +`GNU General Public License `_ +for more details. diff --git a/doc/license.rst b/doc/license.rst deleted file mode 100644 index 9fce89161..000000000 --- a/doc/license.rst +++ /dev/null @@ -1,14 +0,0 @@ -License -******* - -**exSpy** is free software: you can redistribute it and/or modify -it under the terms of the `GNU General Public License (GPL) -`_ as published by -the Free Software Foundation, either version 3 of the license, or -(at your option) any later version. - -**exSpy** is distributed in the hope that it will be useful, -but **without any warranty**; without even the implied warranty of -**merchantability** or **fitness for a particular purpose**. See the -`GNU General Public License `_ -for more details. diff --git a/doc/user_guide/index.rst b/doc/user_guide/index.rst index 9d108c062..4ff2feb63 100644 --- a/doc/user_guide/index.rst +++ b/doc/user_guide/index.rst @@ -5,7 +5,6 @@ User Guide ########## .. toctree:: - :caption: User Guide :maxdepth: 2 install diff --git a/doc/user_guide/install.rst b/doc/user_guide/install.rst index d4904f58b..bd595ae8c 100644 --- a/doc/user_guide/install.rst +++ b/doc/user_guide/install.rst @@ -1,344 +1,117 @@ .. _install-label: -Installing exSpy -================ - -The easiest way to install exSpy is to use the -:ref:`HyperSpy Bundle `, which is available on Windows, MacOS -and Linux. - -Alternatively, exSpy can be installed in an existing python distribution, -read the :ref:`conda installation ` and -:ref:`pip installation` sections for instructions. - -.. _hyperspy-bundle: - -HyperSpy Bundle ---------------- +.. warning:: + These installation instructions are pending the release of the first version of exSpy. + In the meantime, you will need to install the development version, see instructions + below. -The `HyperSpy `__ bundle is very similar -to the Anaconda distribution, and it includes: +Installation +************ - * HyperSpy - * HyperSpyUI - * `HyperSpy extensions `_ - * context `menu shortcut (right-click) `_ - to Jupyter Notebook, Qtconsole or JupyterLab +To install exSpy, you have the following options (independent of the operating system you use): -.. raw:: html +1. exSpy is included in the `HyperSpy Bundle `_, + a standalone program that includes a python distribution and all relevant libraries + (recommended if you do not use *python* for anything else). +2. :ref:`conda` (recommended if you are also working with other *python* packages). +3. :ref:`pip`. +4. Installing the development version from `GitHub `_. + Refer to the appropriate section in the :external+hyperspy:ref:`HyperSpy user guide + ` (replacing ``hyperspy`` by ``exSpy``). -
- - Download HyperSpy-bundle installer - -
-
-For instructions, see the `HyperSpy bundle `__ repository. +.. _conda: Installation using conda ------------------------- +======================== -`Conda `_ is a package manager for Anaconda-like -distributions, such as the `Miniforge `_ -or the `HyperSpy-bundle `__. -Since HyperSpy is packaged in the `conda-forge `__ channel, -it can easily be installed using conda. +Follow these 3 steps to install exSpy using **conda** and start using it. -To install exSpy run the following from the Anaconda Prompt on Windows or -from a Terminal on Linux and Mac. +1. Creating a conda environment +------------------------------- -.. code-block:: bash +exSpy requires Python 3 and ``conda`` -- we suggest using the Python 3 version +of `Miniforge `_. - $ conda install exSpy -c conda-forge +We recommend creating a new environment for the exSpy package (or installing +it in the :external+hyperspy:ref:`HyperSpy ` +environment, if you have one already). To create a new environment: -This will also install the optional GUI packages for exSpy +1. Load the miniforge prompt. +2. Run the following command: .. code-block:: bash - $ conda install hyperspy-base -c conda-forge - -.. note:: - - Depending on how Anaconda has been installed, it is possible that the - ``conda`` command is not available from the Terminal, read the - `Anaconda User Guide `_ for details. - -.. note:: - - Using ``-c conda-forge`` is only necessary when the ``conda-forge`` channel - is not already added to the conda configuration, read the - `conda-forge documentation `_ - for more details. - -.. note:: + (base) conda create -n exspy -y - Depending on the packages installed in Anaconda, ``conda`` can be slow and - in this case ``mamba`` can be used as an alternative of ``conda`` since the - former is significantly faster. Read the - `mamba documentation `_ for instructions. -Further information -^^^^^^^^^^^^^^^^^^^ +2. Installing the package in the new environment +------------------------------------------------ -When installing packages, ``conda`` will verify that all requirements of `all` -packages installed in an environment are met. This can lead to situations where -a solution for dependencies resolution cannot be resolved or the solution may -include installing old or undesired versions of libraries. The requirements -depend on which libraries are already present in the environment as satisfying -their respective dependencies may be problematic. In such a situation, possible -solutions are: - -- use Miniconda instead of Anaconda, if you are installing a python - distribution from scratch: Miniconda only installs very few packages so satisfying - all dependencies is simple. -- install HyperSpy in a `new environment `_. - The following example illustrates how to create a new environment named ``hspy_environment``, - activate it and install HyperSpy in the new environment. +Now activate the exSpy environment and install the package from ``conda-forge``: .. code-block:: bash - $ conda create -n hspy_environment - $ conda activate hspy_environment - $ conda install hyperspy -c conda-forge - -.. note:: - - A consequence of installing hyperspy in a new environment is that you need - to activate this environment using ``conda activate environment_name`` where - ``environment_name`` is the name of the environment, however `shortcuts` can - be created using different approaches: - - - Install `start_jupyter_cm `_ - in the hyperspy environment. - - Install `nb_conda_kernels `_. - - Create `IPython kernels for different environment `_. - -To learn more about the Anaconda eco-system: + (base) conda activate exspy + (exspy) conda install -c conda-forge exspy -y -- Choose between `Anaconda or Miniconda `_? -- Understanding `conda and pip `_. -- What is `conda-forge `__. +Required dependencies will be installed automatically. -.. _install-with-pip: +Installation is completed! To start using it, check the next section. -Installation using pip ----------------------- - -HyperSpy is listed in the `Python Package Index -`_. Therefore, it can be automatically downloaded -and installed `pip `__. You may need to -install pip for the following commands to run. +.. Note:: -To install all of HyperSpy's functionalities, run: + If you run into trouble, check the more detailed documentation in the + :external+hyperspy:ref:`HyperSpy user guide `. -.. code-block:: bash - $ pip install hyperspy[all] +3. Getting Started +------------------ -To install only the strictly required dependencies and limited functionalities, -use: +To get started using exSpy, especially if you are unfamiliar with Python, we +recommend using `Jupyter notebooks `_. Having installed +exSpy as above, a Jupyter notebook can be installed and opened using the following commands +entered into an anaconda prompt (from scratch): .. code-block:: bash - $ pip install hyperspy - -See the following list of selectors to select the installation of optional -dependencies required by specific functionalities: - -* ``learning`` for some machine learning features, -* ``gui-jupyter`` to use the `Jupyter widgets `_ - GUI elements, -* ``gui-traitsui`` to use the GUI elements based on `traitsui `_, -* ``mrcz`` to read mrcz file, -* ``speed`` to speed up some functionalities, -* ``usid`` to read usid file, -* ``tests`` to install required libraries to run HyperSpy's unit tests, -* ``build-doc`` to install required libraries to build HyperSpy's documentation, -* ``dev`` to install all the above, -* ``all`` to install all the above except the development requirements - (``tests``, ``build-doc`` and ``dev``). + (base) conda activate exspy + (exspy) conda install -c conda-forge jupyterlab -y + (exspy) jupyter lab -For example: -.. code-block:: bash - - $ pip install hyperspy[learning, gui-jupyter] - -Finally, be aware that HyperSpy depends on a number of libraries that usually -need to be compiled and therefore installing HyperSpy may require development -tools installed in the system. If the above does not work for you remember that -the easiest way to install HyperSpy is -:ref:`using the HyperSpy bundle `. - -.. _update-with-conda: - -Update HyperSpy ---------------- - -Using conda -^^^^^^^^^^^ - -To update hyperspy to the latest release using conda: - -.. code-block:: bash - - $ conda update hyperspy -c conda-forge - -Using pip -^^^^^^^^^ - -To update hyperspy to the latest release using pip: - -.. code-block:: bash - - $ pip install hyperspy --upgrade - -Install specific version ------------------------- - -Using conda -^^^^^^^^^^^ - -To install a specific version of hyperspy (for example ``1.6.1``) using conda: - -.. code-block:: bash +.. _pip: - $ conda install hyperspy=1.6.1 -c conda-forge - -Using pip -^^^^^^^^^ - -To install a specific version of hyperspy (for example ``1.6.1``) using pip: - -.. code-block:: bash - - $ pip install hyperspy==1.6.1 - - -.. _install-rolling: - -Rolling release Linux distributions ------------------------------------ - -Due to the requirement of up to date versions for dependencies such as *numpy*, -*scipy*, etc., binary packages of HyperSpy are not provided for most linux -distributions and the installation via :ref:`Anaconda/Miniconda ` -or :ref:`Pip ` is recommended. - -However, packages of the latest HyperSpy release and the related -GUI packages are maintained for the rolling release distributions -*Arch-Linux* (in the `Arch User Repository -`_) (AUR) and -*openSUSE* (`Community Package `_) -as ``python-hyperspy`` and ``python-hyperspy-gui-traitsui``, -``python-hyperspy-gui-ipywidgets`` for the GUIs packages. - -A more up-to-date package that contains all updates to be included -in the next minor version release (likely including new features compared to -the stable release) is also available in the AUR as |python-hyperspy-git|_. - -.. |python-hyperspy-git| replace:: ``python-hyperspy-git`` -.. _python-hyperspy-git: https://aur.archlinux.org/packages/python-hyperspy-git - -.. _install-dev: - -Install development version ---------------------------- - -Clone the hyperspy repository -^^^^^^^^^^^^^^^^^^^^^^^^^^^^^ - -To get the development version from our git repository you need to install `git -`_. Then just do: - -.. code-block:: bash - - $ git clone https://github.com/hyperspy/hyperspy.git - -.. Warning:: - - When running hyperspy from a development version, it can happen that the - dependency requirement changes in which you will need to keep this - this requirement up to date (check dependency requirement in ``setup.py``) - or run again the installation in development mode using ``pip`` as explained - below. - -Installation in a Anaconda/Miniconda distribution -^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^ -Optionally, create an environment to separate your hyperspy installation from -other anaconda environments (`read more about environments here -`_): - -.. code-block:: bash - - $ conda create -n hspy_dev python # create an empty environment with latest python - $ conda activate hspy_dev # activate environment - -Install the runtime and development dependencies requirements using conda: - -.. code-block:: bash - - $ conda install hyperspy-base -c conda-forge --only-deps # install hyperspy dependencies - $ conda install hyperspy-dev -c conda-forge # install developer dependencies - -The package ``hyperspy-dev`` will install the development dependencies required -for testing and building the documentation. - -From the root folder of your hyperspy repository (folder containing the -``setup.py`` file) run `pip `_ in development mode: - -.. code-block:: bash - - $ pip install -e . --no-deps # install the currently checked-out branch of hyperspy - -Installation in other (non-system) Python distribution -^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^ +Installation using pip +====================== -From the root folder of your hyperspy repository (folder containing the -``setup.py`` file) run `pip `_ in development mode: +Alternatively, you can also find exSpy in the `Python Package Index (PyPI) `_ +and install it using (requires ``pip``): .. code-block:: bash - $ pip install -e .[dev] - -All required dependencies are automatically installed by pip. If you don't want -to install all dependencies and only install some of the optional dependencies, -use the corresponding selector as explained in the :ref:`install-with-pip` section + pip install exspy -.. - If using Arch Linux, the latest checkout of the master development branch - can be installed through the AUR by installing the `hyperspy-git package - `_ +Required dependencies will be installed automatically. -Installation in a system Python distribution -^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^ -When using a system Python distribution, it is recommended to install the -dependencies using your system package manager. +Updating the package +==================== -From the root folder of your hyperspy repository (folder containing the -``setup.py`` file) run `pip `_ in development mode. +Using **conda**: .. code-block:: bash - $ pip install -e --user .[dev] - -.. _create-debian-binary: - -Creating Debian/Ubuntu binaries -^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^ + conda update exspy -c conda-forge -You can create binaries for Debian/Ubuntu from the source by running the -`release_debian` script +Using **pip**: .. code-block:: bash - $ ./release_debian + pip install exspy --upgrade -.. Warning:: +.. Note:: - For this to work, the following packages must be installed in your system - python-stdeb, debhelper, dpkg-dev and python-argparser are required. + If you want to be notified about new releases, please *Watch (Releases only)* the `exSpy repository + on GitHub `_ (requires a GitHub account). diff --git a/examples/README.rst b/examples/README.rst new file mode 100644 index 000000000..3345ab22f --- /dev/null +++ b/examples/README.rst @@ -0,0 +1,6 @@ +.. _examples-index: + +Gallery of Examples +=================== + +Below is a gallery of examples. diff --git a/examples/model_fitting/EELS_curve_fitting.py b/examples/model_fitting/EELS_curve_fitting.py index d35979758..4087127c8 100644 --- a/examples/model_fitting/EELS_curve_fitting.py +++ b/examples/model_fitting/EELS_curve_fitting.py @@ -17,7 +17,7 @@ beam_energy=300, convergence_angle=24.6, collection_angle=13.6 ) -m = s.create_model(ll=ll) +m = s.create_model(low_loss=ll) m.enable_fine_structure() m.multifit(kind="smart") m.plot() diff --git a/pyproject.toml b/pyproject.toml index fb58f9eb1..99ed3d685 100644 --- a/pyproject.toml +++ b/pyproject.toml @@ -2,4 +2,8 @@ force-exclude = ''' exspy/misc/eds/ffast_mac.py | exspy/misc/elements.py -''' \ No newline at end of file +''' + +[tool.pytest.ini_options] +addopts = "-ra -n auto --dist loadfile" +testpaths = ["hyperspy/tests", ] diff --git a/releasing_guide.md b/releasing_guide.md new file mode 100644 index 000000000..e49f0b764 --- /dev/null +++ b/releasing_guide.md @@ -0,0 +1,35 @@ +# Releasing a new exSpy version + +To publish a new exSpy release do the following steps: + +## Preparation + +- Create a new PR to the 'main' branch for the release process, e.g. `release_v0.1.1` +- Make sure to have the code ready, including changelog +- Set the correct version number in `exSpy/release_info.py` (increase the third + digit for a patch release, the second digit for a regular minor release, the + first digit for a major release) +- Let that PR collect comments for a day to ensure that other maintainers are comfortable + with releasing +- Set correct date and version number in `CHANGES.rst` + +## Tag and Release + +- Create a tag e.g. `git tag -a v0.1.1 -m "exSpy version 0.1.1"` +- Push tag to user fork for a test run `git push origin v0.1.1`. Will run the release + workflow without uploading to PyPi +- Push tag to HoloSpy repository to trigger release `git push upstream v0.1.1` + (this triggers the GitHub action to create the sdist and wheel and upload to + PyPi automatically). :warning: this is a point of no return :warning: + +## Post-release action + +- Increment the version and set it back to dev: `vx.y.zdev0` +- Update version in other branches if necessary +- Prepare `CHANGES.rst` for development by adding `UNRELEASED` headline +- Merge the PR + +## Follow-up + +- Tidy up and close corresponding milestone or project +- A PR to the conda-forge feedstock will be created by the conda-forge bot diff --git a/setup.py b/setup.py index c01b4b373..ca22c17d4 100644 --- a/setup.py +++ b/setup.py @@ -27,10 +27,10 @@ extra_feature_requirements = { "gui-jupyter": [ - "hyperspy_gui_ipywidgets @ git+https://github.com/ericpre/hyperspy_gui_ipywidgets.git@hyperspy2.0", + "hyperspy_gui_ipywidgets @ https://github.com/hyperspy/hyperspy_gui_ipywidgets/archive/hyperspy2.0.zip", ], "gui-traitsui": [ - "hyperspy_gui_traitsui @ git+https://github.com/ericpre/hyperspy_gui_traitsui.git@hyperspy2.0", + "hyperspy_gui_traitsui @ https://github.com/hyperspy/hyperspy_gui_traitsui/archive/hyperspy2.0.zip", ], "doc": [ "numpydoc", @@ -39,13 +39,16 @@ "sphinx-copybutton", "sphinx-design", "sphinx-favicon", + "sphinx-gallery", ], "tests": [ "pytest >= 5.0", "pytest-mpl", "pytest-cov >= 2.8.1", + "pytest-xdist", ], "dev": ["black", "pre-commit >=1.16"], + "all": ["gui-jupyter", "gui-traitsui"], } @@ -56,7 +59,8 @@ author=author, license=license, url="https://github.com/pyxem/pyxem", - long_description=open("README.rst").read(), + long_description=open("README.md").read(), + long_description_content_type="text/markdown", keywords=[ "data analysis", "microscopy", @@ -82,7 +86,7 @@ extras_require=extra_feature_requirements, install_requires=[ "dask[array]", - "hyperspy @ git+https://github.com/hyperspy/hyperspy@RELEASE_next_major", + "hyperspy @ https://github.com/hyperspy/hyperspy/archive/RELEASE_next_major.zip", "matplotlib", "numexpr", "numpy", @@ -95,7 +99,7 @@ ], python_requires="~=3.8", package_data={ - "": ["LICENSE", "README.rst"], + "": ["LICENSE", "README.md"], "exspy": [ "data/*hspy", "test/drawing/data/*hspy",