Initial Settings in the Code (#1)

* environment updated * package name added, mantid logger replaced with python logger, environment updated * configuration, version, and meta updates for new repo * notebooks/ removed, github actions updated * pre-commit errors fixed * coverage and badges * twine check added on github action * prototype script added, excluded from pre-commit * run pytest after package installed in editable mode in github actions, version should exist * pyproject updated to point only to gui, readme update with development installation instructions * readme instruction updates
neutrons · Oct 29, 2024 · 1978169 · 1978169
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diff --git a/.github/workflows/package.yml → .github/workflows/hyspecplanningtools.yml b/.github/workflows/package.yml → .github/workflows/hyspecplanningtools.yml
@@ -7,7 +7,8 @@ on:
     tags: ['v*']
 
 jobs:
-  linux:
+  anaconda-publish:
+    name: upload release to Anaconda
     runs-on: ubuntu-latest
     defaults:
       run:
@@ -20,18 +21,15 @@ jobs:
           channels: conda-forge,defaults
           use-mamba: true
           environment-file: environment.yml
-          activate-environment: test
-      - name: install additional dependencies
-        run: |
-          echo "installing additional dependencies from environment_development.yml"
+          activate-environment: hyspecplanningtools_dev
       - name: build conda package
         run: |
           # set up environment
           cd conda.recipe
           echo "versioningit $(versioningit ../)"
           # build the package
           VERSION=$(versioningit ../) conda mambabuild --channel conda-forge --output-folder . .
-          conda verify noarch/mypackagename*.tar.bz2
+          conda verify noarch/hyspecplanningtools*.tar.bz2
       - name: upload conda package to anaconda
         shell: bash -l {0}
         if: startsWith(github.ref, 'refs/tags/v')
@@ -43,7 +41,7 @@ jobs:
           CONDA_LABEL="main"
           if [ "${IS_RC}" = "true" ]; then CONDA_LABEL="rc"; fi
           echo pushing ${{ github.ref }} with label $CONDA_LABEL
-          anaconda upload --label $CONDA_LABEL conda.recipe/noarch/mypackagename*.tar.bz2
+          anaconda upload --label $CONDA_LABEL conda.recipe/noarch/hyspecplanningtools*.tar.bz2
 
   pypi-publish:
     name: upload release to PyPI
@@ -62,7 +60,7 @@ jobs:
           channels: conda-forge,defaults
           use-mamba: true
           environment-file: environment.yml
-          activate-environment: test
+          activate-environment: hyspecplanningtools_dev
       - name: build pypi package
         run: |
           # build the package

diff --git a/.github/workflows/unittest.yml b/.github/workflows/unittest.yml
@@ -8,7 +8,7 @@ on:
     tags: ['v*']
 
 jobs:
-  linux:
+  pytest_package_tests:
     runs-on: ubuntu-latest
     defaults:
       run:
@@ -21,10 +21,11 @@ jobs:
           channels: conda-forge,defaults
           use-mamba: true
           environment-file: environment.yml
-          activate-environment: test
-      - name: install additional dependencies
+          activate-environment: hyspecplanningtools_dev
+      - name: install in editable mode
         run: |
-          echo "installing additional dependencies if cannot be installed from conda"
+          echo "installing in editable mode"
+          python -m pip install -e .
       - name: run unit tests
         run: |
           echo "running unit tests"
@@ -35,13 +36,18 @@ jobs:
           github.actor != 'dependabot[bot]'
         with:
           token: ${{ secrets.CODECOV_TOKEN }}
+      - name: build python wheel - pypi
+        run: |
+          # test that the python wheel builds
+          VERSION=$(versioningit .) python -m build --wheel --no-isolation
+          twine check dist/hyspecplanningtools-*.whl
       - name: build conda package
         run: |
           # test that the conda package builds
           cd conda.recipe
           echo "versioningit $(versioningit ../)"
           # conda channels could have been defined in the conda-incubator, but you can copy/paste the lines
           # below to build the conda package in your local machine
-          CHANNELS="--channel mantid/label/main --channel conda-forge"
+          CHANNELS="--channel conda-forge"
           VERSION=$(versioningit ../) conda mambabuild $CHANNELS --output-folder . .
-          conda verify noarch/mypackagename*.tar.bz2
+          conda verify noarch/hyspecplanningtools*.tar.bz2
diff --git a/.gitignore b/.gitignore
@@ -25,6 +25,7 @@ share/python-wheels/
 .installed.cfg
 *.egg
 MANIFEST
+_version.py
 
 # PyInstaller
 #  Usually these files are written by a python script from a template

diff --git a/.pre-commit-config.yaml b/.pre-commit-config.yaml
@@ -1,3 +1,5 @@
+exclude: "scripts/.*|.*\\.mat$"
+
 repos:
 - repo: https://github.com/pre-commit/pre-commit-hooks
   rev: v4.6.0

diff --git a/README.md b/README.md
@@ -1,154 +1,27 @@
-python_project_template
-=======================
 
-This repository is a template repository for Python projects under neutrons.
-After you create a new repository using this repo as template, please follow the following steps to adjust it for the new project.
+HyspecPlanningTools
+=====================
 
-Codebase Adjustments
---------------------
+Polarization tool for Single Crystal and Powder
 
-1. Adjust the branch protection rules for the new repo. By default, we should protect the `main` (stable), `qa` (release candidate), and `next` (development) branches.
+## Installation Process
 
-    1.1 Go to the `Settings` tab of the new repo.
+Create the development conda environment
 
-    1.2 Click on `Branches` on the left side.
+`conda env create`
 
-    1.3 Click on `Add rule` button.
+Activate the environment
 
-    1.4 Follow the instructions from Github.
+`conda activate hyspecplanningtools_dev`
 
+Install the application in editable mode
 
-2. Change the License if MIT license is not suitable for you project. For more information about licenses, please
-refer to [Choose an open source license](https://choosealicense.com/).
+`pip install -e .`
 
+Start the tool
 
-3. Update the environment dependency file `environment.yml`, which contain both runtime and development dependencies.
-For more information about conda environment file, please refer to [Conda environment file](https://docs.conda.io/projects/conda/en/latest/user-guide/tasks/manage-environments.html#creating-an-environment-file-manually).
+`hyspecplanningtools`
 
-    3.1 Specify environment 'name' field to match package name
 
-    3.2 We strongly recommended using a single `environment.yml` file to manage all the dependencies, including the runtime and development dependencies.
-
-    3.3 Please add comments to the `environment.yml` file to explain the dependencies.
-
-    3.4 Please prune the dependencies to the minimum when possible, we would like the solver to figure out the dependency tree for us.
-
-
-4. Adjust pre-commit configuration file, `.pre-commit-config.yaml` to enable/disable the hooks you need. For more information about pre-commit, please refer to [pre-commit](https://pre-commit.com/).
-
-
-5. Having code coverage, `codecov.yaml` is **strongly recommended**, please refer to [Code coverage](https://coverage.readthedocs.io/en/coverage-5.5/) for more information.
-
-
-6. Adjust the demo Github action yaml files for CI/CD. For more information about Github action, please refer to [Github action](https://docs.github.com/en/actions).
-
-    6.1 Specify package name at: .github/workflows/package.yml#L34
-
-    6.2 Specify package name at: .github/workflows/package.yml#L46
-
-
-7. Adjust the conda recipe, `conda-recipe/meta.yaml` to provide the meta information for the conda package. For more information about conda recipe, please refer to [Conda build](https://docs.conda.io/projects/conda-build/en/latest/).
-
-    7.1 Specify package name at: conda.recipe/meta.yaml#L15
-
-    7.2 Update license family, if necessary: conda.recipe/meta.yaml#L42
-
-
-8. Adjust `pyproject.toml` to match your project. For more information about `pyproject.toml`,
-please refer to [pyproject.toml](https://www.python.org/dev/peps/pep-0518/).
-
-    8.1 Specify package name at: pyproject.toml#L2
-
-    8.2 Specify package description at: pyproject.toml#L3
-
-    8.3 Specify package name at: pyproject.toml#L39
-
-    8.4 Specify any terminal entry points (terminal commands) at: pyproject.toml#48.
-
-In the example, invoking `packagename-cli` in a terminal is equivalent to running the python script `from packagenamepy.packagename.import main; main()`
-
-    8.5 Projects will use a  single `pyproject.toml` file to manage all the project metadata, including the project name, version, author, license, etc.
-
-    8.6 Python has moved away from `setup.cfg`/`setup.py`, and we would like to follow the trend for our new projects.
-
-
-10. Specify package name at  src/packagenamepy
-
-
-11. Specify package name at: src/packagenamepy/packagename.py
-
-12. If a GUI isn't used, delete the MVP structure at src/packagenamepy:
-    11.1: mainwindow.py
-    11.2: home/
-    11.3: help/
-
-
-11. Clear the content of this file and add your own README.md as the project README file.
-We recommend putting badges of the project status at the top of the README file.
-For more information about badges, please refer to [shields.io](https://shields.io/).
-
-Repository Adjustments
-----------------------
-
-### Add an access token to anaconda
-
-Here we assume your intent is to upload the conda package to the [anaconda.org/neutrons](https://anaconda.org/neutrons) organization.
-An administrator of `anaconda.org/neutrons` must create an access token for your repository in the [access settings](https://anaconda.org/neutrons/settings/access).
-
-After created, the token must be stored in a `repository secret`:
-1. Navigate to the main page of the repository on GitHub.com.
-2. Click on the "Settings" tab.
-3. In the left sidebar, navigate to the "Security" section and select "Secrets and variables" followed by "Actions".
-4. Click on the "New repository secret" button.
-5. Enter `ANACONDA_TOKEN` for the secret name
-6. Paste the Anaconda access token
-7. Click on the "Add secret" button
-8. Test the setup by creating a release candidate tag,
-which will result in a package built and uploaded to https://anaconda.org/neutrons/mypackagename
-
-### Add an access token to codecov
-
-Follow the instructions in the [Confluence page](https://ornl-neutrons.atlassian.net/wiki/spaces/NDPD/pages/103546883/Coverage+reports)
-to create the access token.
-
-Packaging building instructions
--------------------------------
-
-The default package publishing service is anaconda.
-However, we also support PyPI publishing as well.
-
-### Instruction for publish to PyPI
-
-1. Make sure you have the correct access to the project on PyPI.
-2. Make sure `git status` returns a clean state.
-3. At the root of the repo, use `python -m build` to generate the wheel.
-4. Check the wheel with `twine check dist/*`, everything should pass before we move to next step.
-5. When doing manual upload test, make sure to use testpypi instead of pypi.
-6. Use `twine upload --repository testpypi dist/*` to upload to testpypi, you will need to specify the testpipy url in your `~/.pypirc`, i.e.
-
-``````
-[distutils]
-index-servers = pypi, testpypi
-
-[testpypi]
-    repository = https://test.pypi.org/legacy/
-    username = __token__
-    password = YOUR_TESTPYPI_TOKEN
-
-``````
-
-7. Test the package on testpypi with `pip install --index-url https://test.pypi.org/simple/ mypackagename`.
-8. If everything is good, use the Github workflow, `package.yml` to trigger the publishing to PyPI.
-
-### Instruction for publish to Anaconda
-
-Publishing to Anaconda is handled via workflow, `package.yml`.
-
-Development environment setup
------------------------------
-
-### Build development environment
-
-1. By default, we recommend providing a single `environment.yml` that covers all necessary packages for development.
-2. The runtime dependency should be in `meta.yaml` for anaconda packaging, and `pyproject.toml` for PyPI publishing.
-3. When performing editable install for your feature branch, make sure to use `pip install --no-deps -e .` to ensure that `pip` does not install additional packages from `pyproject.toml` into development environment by accident.
+[![CI](https://github.com/neutrons/HyspecPlanningTools/actions/workflows/unittest.yml/badge.svg?branch=next)](https://github.com/neutrons/HyspecPlanningTools/actions/workflows/unittest.yml)
+[![codecov](https://codecov.io/gh/neutrons/HyspecPlanningTools/graph/badge.svg?token=GAQE3SS0HJ)](https://codecov.io/gh/neutrons/HyspecPlanningTools)
diff --git a/conda.recipe/meta.yaml b/conda.recipe/meta.yaml
@@ -12,7 +12,7 @@
 {% set build_number = 0 %}
 
 package:
-  name: mypackagename
+  name: hyspecplanningtools
   version: {{ version_number }}
 
 source:

diff --git a/environment.yml b/environment.yml
@@ -1,23 +1,16 @@
-name: mypythonapp
+name: hyspecplanningtools_dev
 channels:
   - conda-forge
 dependencies:
-  # -- Runtime dependencies
-  # base: list all base dependencies here
-  - python>=3.8  # please specify the minimum version of python here
-  - versioningit
-  # compute: list all compute dependencies here
+  - python>=3.10
+  - pyqt == 5.*
+  - qtpy
   - numpy
-  - pandas
-  # plot: list all plot dependencies here, if applicable
+  - scipy
   - matplotlib
-  # jupyter: list all jupyter dependencies here, if applicable
-  - jupyterlab
-  - ipympl
-  # -- Development dependencies
-  # utils:
   - pre-commit
   # package building:
+  - versioningit
   - libmamba
   - libarchive
   - anaconda-client
@@ -29,16 +22,9 @@ dependencies:
   # docs
   - sphinx
   - sphinx_rtd_theme
+  - sphinxcontrib-mermaid
   - myst-parser  # required for parsing markdown files
   # test: list all test dependencies here
   - pytest
   - pytest-cov
   - pytest-xdist
-  # --------------------------------------------------
-  # add additional sections such as Qt, etc. if needed
-  # --------------------------------------------------
-  # if packages are not available on conda, list them here
-  - pip
-  - pip:
-    - bm3d-streak-removal # example
-    - pytest-playwright
diff --git a/notebooks/example.ipynb b/notebooks/example.ipynb