CI/CD pipeline change and various refactoring/dev (#12)

* Water raman scans processing and viz * Debugging the S3 demo data download * attempting to migrate from circleCI to github actions * attempting to migrate from circleCI to github actions * attempting to migrate from circleCI to github actions * attempting to migrate from circleCI to github actions * attempting to migrate from circleCI to github actions * attempting to migrate from circleCI to github actions * attempting to migrate from circleCI to github actions * Playing with github actions. Publish to pypi on release. * integrating pre-commit and black * getting the GH action linter working * GH action for docs * GH action for docs * Debugging GH action for docs * Debugging GH action for docs * Debugging GH action for docs * increment minor version for new release
drewmee · Oct 31, 2020 · 0f41b69 · 0f41b69
1 parent c8a28b3
commit 0f41b69
Show file tree

Hide file tree

Showing 69 changed files with 3,026 additions and 81,978 deletions.
diff --git a/.circleci/config.yml b/.circleci/config.yml
diff --git a/.github/workflows/docs.yml b/.github/workflows/docs.yml
@@ -0,0 +1,33 @@
+name: Documentation
+
+on:
+  push:
+    paths:
+      - "docs/**"
+      - "README.md"
+      - "CONTRIBUTING.md"
+  pull_request:
+    paths:
+      - "docs/**"
+      - "README.md"
+      - "CONTRIBUTING.md"
+
+jobs:
+  build:
+    runs-on: ubuntu-latest
+
+    steps:
+      - uses: actions/checkout@v2
+
+      - name: Set up Python 3.6
+        uses: actions/setup-python@v2
+        with:
+          python-version: 3.6
+
+      - name: Install dependencies
+        run: |
+          sudo apt-get install pandoc
+          python -m pip install --upgrade pip setuptools wheel
+          pip install -e ".[docs, jupyter]"
+      - name: Build documentation
+        run: sphinx-build -a -b html -W docs/source/ docs/build/
diff --git a/.github/workflows/lint.yml b/.github/workflows/lint.yml
@@ -0,0 +1,13 @@
+name: Lint
+
+on: [push, pull_request]
+
+jobs:
+  lint:
+    runs-on: ubuntu-latest
+    steps:
+      - uses: actions/checkout@v2
+      - uses: actions/setup-python@v2
+        with:
+          python-version: 3.6
+      - uses: psf/black@stable
diff --git a/.github/workflows/pypi_publish.yml b/.github/workflows/pypi_publish.yml
@@ -0,0 +1,31 @@
+# This workflows will upload a Python Package using Twine when a release is created
+# For more information see: https://help.github.com/en/actions/language-and-framework-guides/using-python-with-github-actions#publishing-to-package-registries
+
+name: Upload Python Package
+
+on:
+  release:
+    types: [created]
+
+jobs:
+  deploy:
+
+    runs-on: ubuntu-latest
+
+    steps:
+    - uses: actions/checkout@v2
+    - name: Set up Python
+      uses: actions/setup-python@v2
+      with:
+        python-version: '3.x'
+    - name: Install dependencies
+      run: |
+        python -m pip install --upgrade pip
+        pip install setuptools wheel twine
+    - name: Build and publish
+      env:
+        TWINE_USERNAME: ${{ secrets.PYPI_USERNAME }}
+        TWINE_PASSWORD: ${{ secrets.PYPI_PASSWORD }}
+      run: |
+        python setup.py sdist bdist_wheel
+        twine upload dist/*
diff --git a/.github/workflows/test.yml b/.github/workflows/test.yml
@@ -0,0 +1,29 @@
+# This workflow will install Python dependencies, run tests and lint with a variety of Python versions
+# For more information see: https://help.github.com/actions/language-and-framework-guides/using-python-with-github-actions
+
+name: Test
+
+on: [push, pull_request]
+
+jobs:
+  build:
+
+    runs-on: ubuntu-latest
+    strategy:
+      matrix:
+        python-version: [3.6, 3.7, 3.8]
+        os: ['ubuntu-latest', 'macos-latest', 'windows-latest']
+
+    steps:
+    - uses: actions/checkout@v2
+    - name: Set up Python ${{ matrix.python-version }}
+      uses: actions/setup-python@v2
+      with:
+        python-version: ${{ matrix.python-version }}
+    - name: Install dependencies
+      run: |
+        python -m pip install --upgrade pip
+        pip install -e .[tests]
+    - name: Test with pytest
+      run: |
+        pytest -v
diff --git a/.gitignore b/.gitignore
@@ -143,4 +143,5 @@ cython_debug/
 # Temporary data for demo datasets
 docs/source/tutorials/notebooks/demo_data/
 !.gitkeep
-local_test_data/
+local_test_data/
+local_dev_notebooks/
diff --git a/.pre-commit-config.yaml b/.pre-commit-config.yaml
@@ -0,0 +1,6 @@
+repos:
+  - repo: https://github.com/psf/black
+    rev: 20.8b1 # Replace by any tag/version: https://github.com/psf/black/tags
+    hooks:
+      - id: black
+        language_version: python3 # Should be a command that runs python3.6+
diff --git a/README.md b/README.md
@@ -1,11 +1,12 @@
 # PyEEM
 
-[![pypi version](https://img.shields.io/pypi/v/pyeem.svg 'pypi version')](https://pypi.org/project/pyeem/)
-[![PyPI - Python Version](https://img.shields.io/pypi/pyversions/pyeem.svg)](https://pypi.org/project/pyeem/)
-[![CircleCI](https://circleci.com/gh/drewmee/PyEEM.svg?style=shield&circle-token=ccdb16078dcb8ee4e4c9b923f547fc7cb2742aae)](https://app.circleci.com/pipelines/github/drewmee/PyEEM)
+![Test](https://github.com/drewmee/PyEEM/workflows/Test/badge.svg)
 [![Read the Docs](https://readthedocs.org/projects/pyeem/badge/?version=latest)](https://pyeem.readthedocs.io/)
+[![PyPi version](https://img.shields.io/pypi/v/pyeem.svg 'pypi version')](https://pypi.org/project/pyeem/)
+[![PyPI - Python Version](https://img.shields.io/pypi/pyversions/pyeem.svg)](https://pypi.org/project/pyeem/)
 [![Binder](https://mybinder.org/badge.svg)](https://mybinder.org/v2/gh/drewmee/PyEEM/master?filepath=docs%2Fsource%2Ftutorials%2Fnotebooks)
-[![license](https://img.shields.io/github/license/mashape/apistatus.svg)](https://github.com/drewmee/PyEEM/blob/master/LICENSE)
+[![License](https://img.shields.io/github/license/mashape/apistatus.svg)](https://github.com/drewmee/PyEEM/blob/master/LICENSE)
+[![Code style](https://img.shields.io/badge/code%20style-black-000000.svg)](https://github.com/psf/black)
 <!--- Badge for codecov -->
 
 Python library for the preprocessing, analysis, and visualization of Excitation Emission Matrices (EEMs).

diff --git a/docs/source/api/pyeem.augmentation.create_mixture_spectra.rst b/docs/source/api/pyeem.augmentation.create_mixture_spectra.rst
@@ -0,0 +1,6 @@
+create_mixture_spectra
+======================
+
+.. currentmodule:: pyeem.augmentation
+
+.. autofunction:: create_mixture_spectra
diff --git a/docs/source/api/pyeem.augmentation.create_mixtures.rst b/docs/source/api/pyeem.augmentation.create_mixtures.rst
diff --git a/docs/source/api/pyeem.augmentation.prototypical_spectrum.rst b/docs/source/api/pyeem.augmentation.prototypical_spectrum.rst
diff --git a/docs/source/api/pyeem.augmentation.single_source.rst b/docs/source/api/pyeem.augmentation.single_source.rst
diff --git a/docs/source/api/pyeem.instruments.tecan.Spark.rst b/docs/source/api/pyeem.instruments.tecan.Spark.rst
@@ -0,0 +1,37 @@
+Spark
+=====
+
+.. currentmodule:: pyeem.instruments.tecan
+
+.. autoclass:: Spark
+   :show-inheritance:
+
+   .. rubric:: Attributes Summary
+
+   .. autosummary::
+
+      ~Spark.manufacturer
+      ~Spark.name
+      ~Spark.supported_models
+
+   .. rubric:: Methods Summary
+
+   .. autosummary::
+
+      ~Spark.load_absorbance
+      ~Spark.load_eem
+      ~Spark.load_spectral_corrections
+      ~Spark.load_water_raman
+
+   .. rubric:: Attributes Documentation
+
+   .. autoattribute:: manufacturer
+   .. autoattribute:: name
+   .. autoattribute:: supported_models
+
+   .. rubric:: Methods Documentation
+
+   .. automethod:: load_absorbance
+   .. automethod:: load_eem
+   .. automethod:: load_spectral_corrections
+   .. automethod:: load_water_raman
diff --git a/docs/source/api/pyeem.plots.absorbance_plot.rst b/docs/source/api/pyeem.plots.absorbance_plot.rst
@@ -0,0 +1,6 @@
+absorbance_plot
+===============
+
+.. currentmodule:: pyeem.plots
+
+.. autofunction:: absorbance_plot
diff --git a/docs/source/api/pyeem.plots.calibration_curves_plot.rst b/docs/source/api/pyeem.plots.calibration_curves_plot.rst
@@ -0,0 +1,6 @@
+calibration_curves_plot
+=======================
+
+.. currentmodule:: pyeem.plots
+
+.. autofunction:: calibration_curves_plot
diff --git a/docs/source/api/pyeem.plots.model_history_plot.rst b/docs/source/api/pyeem.plots.model_history_plot.rst
@@ -0,0 +1,6 @@
+model_history_plot
+==================
+
+.. currentmodule:: pyeem.plots
+
+.. autofunction:: model_history_plot
diff --git a/docs/source/api/pyeem.plots.plot_calibration_curves.rst b/docs/source/api/pyeem.plots.plot_calibration_curves.rst
diff --git a/docs/source/api/pyeem.plots.plot_preprocessing.rst b/docs/source/api/pyeem.plots.plot_preprocessing.rst
diff --git a/docs/source/api/pyeem.plots.plot_prototypical_spectra.rst b/docs/source/api/pyeem.plots.plot_prototypical_spectra.rst
diff --git a/docs/source/api/pyeem.plots.prediction_parity_plot.rst b/docs/source/api/pyeem.plots.prediction_parity_plot.rst
@@ -0,0 +1,6 @@
+prediction_parity_plot
+======================
+
+.. currentmodule:: pyeem.plots
+
+.. autofunction:: prediction_parity_plot
diff --git a/docs/source/api/pyeem.plots.preprocessing_routine_plot.rst b/docs/source/api/pyeem.plots.preprocessing_routine_plot.rst
@@ -0,0 +1,6 @@
+preprocessing_routine_plot
+==========================
+
+.. currentmodule:: pyeem.plots
+
+.. autofunction:: preprocessing_routine_plot
diff --git a/docs/source/api/pyeem.plots.prototypical_spectra_plot.rst b/docs/source/api/pyeem.plots.prototypical_spectra_plot.rst
@@ -0,0 +1,6 @@
+prototypical_spectra_plot
+=========================
+
+.. currentmodule:: pyeem.plots
+
+.. autofunction:: prototypical_spectra_plot
diff --git a/docs/source/api/pyeem.plots.water_raman_peak_animation.rst b/docs/source/api/pyeem.plots.water_raman_peak_animation.rst
@@ -0,0 +1,6 @@
+water_raman_peak_animation
+==========================
+
+.. currentmodule:: pyeem.plots
+
+.. autofunction:: water_raman_peak_animation
diff --git a/docs/source/api/pyeem.plots.water_raman_peak_plot.rst b/docs/source/api/pyeem.plots.water_raman_peak_plot.rst
@@ -0,0 +1,6 @@
+water_raman_peak_plot
+=====================
+
+.. currentmodule:: pyeem.plots
+
+.. autofunction:: water_raman_peak_plot
diff --git a/docs/source/api/pyeem.plots.water_raman_timeseries.rst b/docs/source/api/pyeem.plots.water_raman_timeseries.rst
@@ -0,0 +1,6 @@
+water_raman_timeseries
+======================
+
+.. currentmodule:: pyeem.plots
+
+.. autofunction:: water_raman_timeseries
diff --git a/docs/source/api/pyeem.preprocessing.filters.fill_missing_values.rst b/docs/source/api/pyeem.preprocessing.filters.fill_missing_values.rst
@@ -0,0 +1,6 @@
+fill_missing_values
+===================
+
+.. currentmodule:: pyeem.preprocessing.filters
+
+.. autofunction:: fill_missing_values
diff --git a/docs/source/changelog.rst b/docs/source/changelog.rst
@@ -6,7 +6,14 @@
 Release Notes
 *************
 
-Version 0.1 (2020-08-DD)
+Version 0.1.1 (2020-08-26)
+--------------------------
+
+**New Features**:
+
+- Minor bug fixes.
+
+Version 0.1.0 (2020-08-19)
 --------------------------
 
 **New Features**:

diff --git a/docs/source/contributing.rst b/docs/source/contributing.rst
@@ -6,21 +6,21 @@
 Contributing
 ************
 
-PyEEM is an open-source project and contributions are always welcome from anyone. Feel free to open a pull request on `GitHub <https://github.com/drewmee/PyEEM>`_ or file a new feature request or bug report on our `issue tracker <https://github.com/drewmee/PyEEM/issues>`_.
+PyEEM is an open-source project and contributions are always welcome from anyone. Feel free to open a pull request on `GitHub <https://github.com/drewmee/PyEEM>`__ or file a new feature request or bug report on our `issue tracker <https://github.com/drewmee/PyEEM/issues>`__.
 
 
 ==================
 Contributing guide
 ==================
 
-If you are new to working with forks, check out `GitHub's working with forks article <https://help.github.com/articles/working-with-forks/>`_.
+If you are new to working with forks, check out `GitHub's working with forks article <https://help.github.com/articles/working-with-forks/>`__.
 
 
 Step 1: Creating a new issue
 ============================
 
-- If you don't already have a `GitHub <http://www.github.com>`_ account, create one
-- Go to the `PyEEM GitHub page <https://github.com/drewmee/PyEEM>`_ and create a new issue by clicking on the "Issues" tab and then the "New issue" button
+- If you don't already have a `GitHub <http://www.github.com>`__ account, create one
+- Go to the `PyEEM GitHub page <https://github.com/drewmee/PyEEM>`__ and create a new issue by clicking on the "Issues" tab and then the "New issue" button
 
 .. image:: _static/open-new-issue.png
 
@@ -139,7 +139,7 @@ The output should be
 Step 6: Install local copy of PyEEM
 ======================================
 
-Next, you'll want to make sure that Python imports your local version of PyEEM. This can be done by ``pip`` installing your local PyEEM repository in `editable mode <https://pip.pypa.io/en/stable/reference/pip_install/#editable-installs>`_
+Next, you'll want to make sure that Python imports your local version of PyEEM. This can be done by ``pip`` installing your local PyEEM repository in `editable mode <https://pip.pypa.io/en/stable/reference/pip_install/#editable-installs>`__
 
 .. code-block:: bash
 
@@ -219,7 +219,7 @@ Finally, you can go to your copy of PyEEM on GitHub and submit a pull
 request by clicking the "Compare & pull request" button!
 
 If you're new to writing pull requests, see GitHub's `How to write the perfect
-pull request <https://blog.github.com/2015-01-21-how-to-write-the-perfect-pull-request/>`_
+pull request <https://blog.github.com/2015-01-21-how-to-write-the-perfect-pull-request/>`__
 article for a list of some best practices.
 
 .. image:: _static/pull-request-button.png
diff --git a/docs/source/subpackages/instruments/index.rst b/docs/source/subpackages/instruments/index.rst
@@ -7,6 +7,7 @@ The *instruments* subpackage provides functions to load demo and custom datasets
 
    agilent/index
    horiba/index
+   tecan/index
 
 .. automodapi:: pyeem.instruments
    :no-inheritance-diagram:
diff --git a/docs/source/subpackages/instruments/tecan/index.rst b/docs/source/subpackages/instruments/tecan/index.rst
@@ -0,0 +1,6 @@
+Tecan (pyeem.instruments.tecan)
+=================================
+The *instruments.tecan* package provides...
+
+.. automodapi:: pyeem.instruments.tecan
+   :no-inheritance-diagram:
diff --git a/docs/source/tutorials/notebooks/demo_data/.gitkeep b/docs/source/tutorials/notebooks/demo_data/.gitkeep