Modernize project setup (#164)

* Change to more modern project setup

* Move notebooks to docs, automatically render

* Update GH actions to use hatch

* Remove cli.py (unused). Update readme

* Add klapo as contributor. Update changelog

* Update bumpversion cfg

* Bump version: 1.1.2 → 1.2.0

* Add version, date to changelog

* Remove cli/main from tests

* Pin pandas to <2

.bumpversion.cfg

@@ -1,12 +1,8 @@
 [bumpversion]
-current_version = 1.1.2
+current_version = 1.2.0
 commit = True
 tag = True
 
-[bumpversion:file:setup.py]
-search = version='{current_version}'
-replace = version='{new_version}'
-
 [bumpversion:file:README.rst]
 search = v{current_version}.
 replace = v{new_version}.

.github/workflows/build.yml

@@ -27,12 +27,10 @@ jobs:
           python3 --version
       - name: Upgrade pip and install dependencies
         run: |
-          python3 -m pip install --upgrade pip setuptools
-          python3 -m pip install .[dev,publishing]
-      - name: Check style against standards using flake8
-        run: flake8 src tests setup.py
-      - name: Check import order
-        run: isort --check-only src/dtscalibration --diff
+          python3 -m pip install --upgrade pip hatch
+          python3 -m pip install .[dev]
+      - name: Check style with Ruff and isort
+        run: hatch run lint
 
   build:
     name: Build for (${{ matrix.python-version }}, ${{ matrix.os }})
@@ -55,9 +53,9 @@ jobs:
           python3 --version
       - name: Upgrade pip and install dependencies
         run: |
-          python3 -m pip install --upgrade pip setuptools
-          python3 -m pip install .[dev,publishing]
+          python3 -m pip install --upgrade pip hatch
+          python3 -m pip install .[dev]
       - name: Run unit tests
-        run: pytest -v
+        run: hatch run test
       - name: Verify that we can build the package
-        run: python3 setup.py sdist bdist_wheel
+        run: hatch build

.github/workflows/documentation.yml

@@ -27,11 +27,9 @@ jobs:
           python3 --version
       - name: Upgrade pip and install dependencies
         run: |
-          python3 -m pip install --upgrade pip setuptools
+          python3 -m pip install --upgrade pip hatch
           python3 -m pip install .[docs]
       - name: Install pandoc using apt
         run: sudo apt install pandoc
-      - name: Convert the notebook examples to docs
-        run: python docs/nb_examples_to_docs.py
       - name: Build documentation
-        run: sphinx-build -b html docs dist/docs
+        run: hatch run docs:build

.readthedocs.yml

@@ -15,7 +15,9 @@ build:
 sphinx:
    configuration: docs/conf.py
 
-# Optionally declare the Python requirements required to build your docs
 python:
-   install:
-   - requirements: docs/requirements.txt
+  install:
+    - method: pip
+      path: .
+      extra_requirements:
+        - docs

AUTHORS.rst

@@ -4,3 +4,4 @@ Authors
 
 * Bas des Tombe - https://github.com/bdestombe
 * Bart Schilperoort - https://github.com/BSchilperoort
+* Karl Lapo - https://github.com/klapo

CHANGELOG.rst

@@ -1,6 +1,26 @@
 
 Changelog
 =========
+[1.2.0] (13-03-2023)
+
+Bugfixes
+
+* Fixed deprecated np.float and np.int
+
+Other
+
+* Moved project build system & scripts to hatch.
+* Project is now fully configured using pyproject.toml
+* Linting is handled by Ruff.
+* Notebooks are now rendered as part of the documentation.
+
+Removed
+
+* cli.py script (unused) has been removed.
+
+New contributors:
+* Karl Lapo (@klapo)
+
 1.1.2 (2022-09-25)
 ------------------
 

CITATION.cff

@@ -22,5 +22,5 @@ doi: "10.5281/zenodo.1410097"
 license: "BSD-3-Clause"
 repository-code: "https://github.com/dtscalibration/python-dts-calibration"
 title: "Python distributed temperature sensing calibration"
-version: "v1.1.2"
+version: "v1.2.0"
 url: "https://python-dts-calibration.readthedocs.io"

CONTRIBUTING.rst

@@ -8,7 +8,7 @@ little bit helps, and credit will always be given.
 Bug reports
 ===========
 
-When `reporting a bug <https://github.com/bdestombe/python-dts-calibration/issues>`_ please include:
+When `reporting a bug <https://github.com/dtscalibration/python-dts-calibration/issues>`_ please include:
 
     * Your operating system name and version.
     * Any details about your local setup that might be helpful in troubleshooting.
@@ -24,7 +24,7 @@ articles, and such.
 Feature requests and feedback
 =============================
 
-The best way to send feedback is to file an issue at https://github.com/bdestombe/python-dts-calibration/issues.
+The best way to send feedback is to file an issue at https://github.com/dtscalibration/python-dts-calibration/issues.
 
 If you are proposing a feature:
 
@@ -37,7 +37,7 @@ Development
 
 To set up `python-dts-calibration` for local development:
 
-1. Fork `python-dts-calibration <https://github.com/bdestombe/python-dts-calibration>`_
+1. Fork `python-dts-calibration <https://github.com/dtscalibration/python-dts-calibration>`_
    (look for the "Fork" button).
 2. Clone your fork locally::
 
@@ -49,9 +49,15 @@ To set up `python-dts-calibration` for local development:
 
    Now you can make your changes locally.
 
-4. When you're done making changes, run all the checks, doc builder and spell checker with `tox <http://tox.readthedocs.io/en/latest/install.html>`_ one command::
+4. Activate your desired development environment (e.g., a python venv or conda environment), and install the package in editable mode, with the dev dependencies::
 
-    tox
+    pip install -e .[dev]
+
+4. When you're done making changes, make sure the code follows the right style, that all tests pass, and that the docs build with the following commands::
+
+    hatch run format
+    hatch run test
+    hatch run docs:build
 
 5. Commit your changes and push your branch to GitHub::
 
@@ -68,23 +74,19 @@ If you need some code review or feedback while you're developing the code just m
 
 For merging, you should:
 
-1. Include passing tests (run ``tox``) [1]_.
+1. Include passing tests (do ``hatch run test``) [1]_.
 2. Update documentation when there's new API, functionality etc.
 3. Add a note to ``CHANGELOG.rst`` about the changes.
 4. Add yourself to ``AUTHORS.rst``.
 
-.. [1] If you don't have all the necessary python versions available locally you can rely on Travis - it will
-       `run the tests <https://travis-ci.org/bdestombe/python-dts-calibration/pull_requests>`_ for each change you add in the pull request.
-
-       It will be slower though ...
+.. [1] Sometimes there are issues with different python versions. For this you can do
+       ``hatch run test_matrix:test``. Generally, on Github tests will be run using Github Actions,
+       where all versions, as well as the documentation, are tested.
+       This will be slower though ...
 
 Tips
 ----
 
 To run a subset of tests::
 
-    tox -e envname -- pytest -k test_myfeature
-
-To run all the test environments in *parallel* (you need to ``pip install detox``)::
-
-    detox
+    hatch run pytest -k test_myfeature

README.rst

@@ -29,7 +29,7 @@ Overview
     :alt: PyPI Package latest release
     :target: https://pypi.python.org/pypi/dtscalibration
 
-.. |commits-since| image:: https://img.shields.io/github/commits-since/dtscalibration/python-dts-calibration/v1.1.2.svg
+.. |commits-since| image:: https://img.shields.io/github/commits-since/dtscalibration/python-dts-calibration/v1.2.0.svg
     :alt: Commits since latest release
     :target: https://github.com/dtscalibration/python-dts-calibration/compare/v1.1.1...main
 
@@ -45,10 +45,6 @@ Overview
    :alt: It would be greatly appreciated if you could cite this package in eg articles presentations
    :target: https://zenodo.org/badge/latestdoi/143077491
 
-.. |example-notebooks| image:: https://mybinder.org/badge.svg
-   :alt: Interactively run the example notebooks online
-   :target: https://mybinder.org/v2/gh/dtscalibration/python-dts-calibration/main?filepath=examples%2Fnotebooks
-
 .. end-badges
 
 A Python package to load Distributed Temperature Sensing files, perform a calibration, and plot the result. A detailed description of the calibration procedure can be found at https://doi.org/10.3390/s20082235 .
@@ -90,14 +86,12 @@ Devices currently supported
 * AP Sensing: **CP320** .xml files *(single ended only)*
 * SensorTran: **SensorTran 5100** .dat binary files *(single ended only)*
 
-Learn by examples
-=================
-Interactively run the example notebooks online by clicking `here <https://mybinder.org/v2/gh/dtscalibration/python-dts-calibration/main?filepath=examples%2Fnotebooks>`_.
-
 Documentation
 =============
 
 https://python-dts-calibration.readthedocs.io/
+Example notebooks can be viewed [here](https://python-dts-calibration.readthedocs.io/en/latest/learn_by_examples.html).
+
 
 How to cite
 ===========

docs/conf.py

@@ -14,7 +14,7 @@
     'sphinx.ext.todo',
     'sphinx.ext.viewcode',
     'sphinx.ext.autosectionlabel',
-    # 'nbsphinx',
+    'nbsphinx',
     'sphinx.ext.mathjax',
     'sphinx.ext.intersphinx',
     'sphinx_automodapi.automodapi',
@@ -30,7 +30,7 @@
     ]
 
 if os.getenv('SPELLCHECK'):
-    extensions += 'sphinxcontrib.spelling',
+    extensions += 'sphinxcontrib.spelling'
     spelling_show_suggestions = True
     spelling_lang = 'en_US'
 
@@ -41,7 +41,7 @@
 year = str(date.today().year)
 author = 'Bas des Tombe and Bart Schilperoort'
 copyright = '{0}, {1}'.format(year, author)
-version = release = '1.1.2'
+version = release = '1.2.0'
 
 pygments_style = 'trac'
 templates_path = ['.']
@@ -69,3 +69,7 @@
 
 # sphinx_automodapi.automodapi
 numpydoc_show_class_members = False
+
+# -- nbsphinx configuration --
+nbsphinx_allow_errors = False
+nbsphinx_execute = "always"