Merge branch 'master' into dependabot/pip/pillow-9.3.0

.coveragerc

@@ -0,0 +1,13 @@
+[run]
+source = pyreduce
+omit =
+    pyreduce/_version.py
+    examples/*
+    versioneer.py
+    setup.py
+
+[report]
+show_missing = True
+
+[xml]
+output = cov.xml

.flake8

@@ -0,0 +1,6 @@
+[flake8]
+max-line-length = 88
+max-complexity = 18
+# select = B,C,E,F,W,T4,B9
+ignore = E203, E266, E501, W503, F403, F401
+select = E9,F63,F7,F82

.gitattributes

@@ -0,0 +1 @@
+pyreduce/_version.py export-subst

.github/workflows/python-publish.yml

@@ -0,0 +1,99 @@
+# This workflow will install Python dependencies, run tests and lint with a single version of Python
+# For more information see: https://help.github.com/actions/language-and-framework-guides/using-python-with-github-actions
+
+name: Python application
+
+on:
+  push:
+    branches: [ master ]
+  pull_request:
+    branches: [ master ]
+
+jobs:
+  build:
+    runs-on: ubuntu-latest
+
+    steps:
+    - uses: actions/checkout@v2
+
+    - name: Set up Python 3.8
+      uses: actions/setup-python@v2
+      with:
+        python-version: 3.8
+
+    - name: Install dependencies
+      run: |
+        python -m pip install --upgrade pip
+        pip install flake8 pytest
+        if [ -f requirements.txt ]; then pip install -r requirements.txt; fi
+        pip install .
+
+    - name: Lint with flake8
+      run: |
+        # stop the build if there are Python syntax errors or undefined names
+        flake8 . --count --select=E9,F63,F7,F82 --show-source --statistics
+        # exit-zero treats all errors as warnings. The GitHub editor is 127 chars wide
+        flake8 . --count --exit-zero --max-complexity=10 --max-line-length=127 --statistics
+
+    - name: Test with pytest
+      run: pytest
+
+  deploy:
+    runs-on: ubuntu-latest
+    needs: [build]
+    if: github.event_name == 'push'
+    steps:
+    - uses: actions/checkout@v2
+
+    - name: GitHub Tag
+      id: tag_release
+      uses: mathieudutour/github-tag-action@v5
+      with:
+        github_token: ${{ secrets.GITHUB_TOKEN }}
+
+    - uses: actions/checkout@v2
+      with:
+        ref:  ${{ steps.tag_release.outputs.new_tag }}
+        clean: true
+
+    - name: Set up Python 3.8
+      uses: actions/setup-python@v2
+      with:
+        python-version: 3.8
+
+    - name: Build Wheel
+      run: pip install wheel && python setup.py sdist
+
+    - name: Zip data
+      id: zip_data
+      run: |
+        zip -r dist dist &&
+        echo "::set-output name=filename::dist.zip"
+
+    - name: Create Release
+      id: create_release
+      uses: actions/create-release@v1
+      env:
+        GITHUB_TOKEN: ${{ secrets.GITHUB_TOKEN }} # This token is provided by Actions, you do not need to create your own token
+      with:
+        tag_name: ${{ steps.tag_release.outputs.new_tag }}
+        release_name: Release ${{ steps.tag_release.outputs.new_tag }}
+        draft: false
+        prerelease: false
+
+    - name: Upload Release Asset
+      id: upload-release-asset
+      uses: actions/upload-release-asset@v1
+      env:
+        GITHUB_TOKEN: ${{ secrets.GITHUB_TOKEN }}
+      with:
+        upload_url: ${{ steps.create_release.outputs.upload_url }} # This pulls from the CREATE RELEASE step above, referencing it's ID to get its outputs object, which include a `upload_url`. See this blog post for more info: https://jasonet.co/posts/new-features-of-github-actions/#passing-data-to-future-steps
+        asset_path: ./dist.zip
+        asset_name: dist.zip
+        asset_content_type: application/zip
+
+    - name: Publish a Python distribution to PyPI
+      uses: pypa/gh-action-pypi-publish@master
+      with:
+        user: __token__
+        password: ${{ secrets.pypi_password }}

.pre-commit-config.yaml

@@ -0,0 +1,43 @@
+repos:
+-   repo: https://github.com/pre-commit/pre-commit-hooks
+    rev: v4.0.1
+    hooks:
+    # Identify invalid files
+    -   id: check-ast
+    -   id: check-yaml
+    -   id: check-json
+    -   id: check-toml
+    # git checks
+    -   id: check-merge-conflict
+    -   id: check-added-large-files
+    -   id: detect-private-key
+    -   id: check-case-conflict
+    # Python checks
+    -   id: check-docstring-first
+    -   id: debug-statements
+    -   id: requirements-txt-fixer
+    -   id: fix-encoding-pragma
+    -   id: fix-byte-order-marker
+    # General checks
+    -   id: mixed-line-ending
+        exclude: ".fits"
+    -   id: trailing-whitespace
+        exclude: ".fits"
+    # -   id: check-executables-have-shebangs
+    -   id: end-of-file-fixer
+-   repo: https://github.com/asottile/pyupgrade
+    rev: v2.29.0
+    hooks:
+    -   id: pyupgrade
+-   repo: https://github.com/pycqa/isort
+    rev: 5.9.3
+    hooks:
+      - id: isort
+-   repo: https://github.com/psf/black
+    rev: 21.9b0
+    hooks:
+    -   id: black
+-   repo: https://github.com/PyCQA/flake8
+    rev:  4.0.1
+    hooks:
+    -   id: flake8

.pyup.yml

@@ -1,4 +1,4 @@
-# autogenerated pyup.io config file 
+# autogenerated pyup.io config file
 # see https://pyup.io/docs/configuration/ for all available options
 
 schedule: every month

.readthedocs.yaml

@@ -0,0 +1,19 @@
+# .readthedocs.yml
+# Read the Docs configuration file
+# See https://docs.readthedocs.io/en/stable/config-file/v2.html for details
+
+# Required
+version: 2
+
+# Build documentation in the docs/ directory with Sphinx
+sphinx:
+  configuration: docs/conf.py
+
+# Optionally build your docs in additional formats such as PDF and ePub
+formats: all
+
+# Optionally set the version of Python and requirements required to build your docs
+python:
+  version: "3"
+  install:
+    - requirements: docs/requirements.txt

MANIFEST.in

@@ -7,9 +7,14 @@ include pyreduce/clib/slit_func_2d_xi_zeta_bd.h
 
 include pyreduce/instruments/*.json
 include pyreduce/settings/*.json
-include examples/*.json
 include test/settings/*.json
 
 include pyreduce/masks/*.gz
 
-include pyreduce/wavecal/*npz
+include pyreduce/wavecal/*npz
+
+include setup.cfg
+include versioneer.py
+include pyreduce/_version.py
+
+include codemeta.json

README.md

@@ -1,7 +1,9 @@
-[![Build Status](https://travis-ci.org/AWehrhahn/PyReduce.svg?branch=master)](https://travis-ci.org/AWehrhahn/PyReduce)
+![Python application](https://github.com/AWehrhahn/PyReduce/workflows/Python%20application/badge.svg)
 [![Documentation Status](https://readthedocs.org/projects/pyreduce-astro/badge/?version=latest)](https://pyreduce-astro.readthedocs.io/en/latest/?badge=latest)
 [![Updates](https://pyup.io/repos/github/AWehrhahn/PyReduce/shield.svg)](https://pyup.io/repos/github/AWehrhahn/PyReduce/)
 
+# PyReduce is not currently under development and is provided as is. If you want to take over the project, please contact me.
+
 # PyREDUCE
 
 PyReduce is a port of the [REDUCE](http://www.astro.uu.se/~piskunov/RESEARCH/REDUCE/) package to Python3.
@@ -13,6 +15,15 @@ Installation
 ------------
 PyReduce can be installed using pip using the following command: ``pip install pyreduce-astro``
 
+The most up-to-date version can be installed using ``pip install git+https://github.com/AWehrhahn/PyReduce`` instead. However this may be more buggy than the stable version.
+
+PyReduce uses CFFI to link to the C code, on non-linux platforms you might have to install libffi.
+See also https://cffi.readthedocs.io/en/latest/installation.html#platform-specific-instructions for details.
+
+Output Format
+-------------
+PyReduce will create ``.ech`` files when run. Despite the name those are just regular ``.fits`` files and can be opened with any programm that can read ``.fits``. The data is contained in a table extension. The header contains all the keywords of the input science file, plus some extra PyReduce specific keyword, all of which start with ``e_``.
+
 How To
 ------
 PyReduce is designed to be easy to use, but still be flexible.
@@ -27,4 +38,4 @@ Papers
 ------
 The original REDUCE paper: [doi:10.1051/0004-6361:20020175](https://doi.org/10.1051/0004-6361:20020175)
 
-A paper describing the changes and updates of PyReduce is in preperation.
+A paper describing the changes and updates of PyReduce can be found here: [https://ui.adsabs.harvard.edu/abs/2021A%26A...646A..32P/abstract](https://ui.adsabs.harvard.edu/abs/2021A%26A...646A..32P/abstract)

codemeta.json

@@ -0,0 +1,53 @@
+{
+    "@context": [
+        "https://doi.org/10.5063/schema/codemeta-2.0",
+        "http://schema.org",
+        {
+            "entryPoints": {
+                "@reverse": "schema:actionApplication"
+            },
+            "interfaceType": {
+                "@id": "codemeta:interfaceType"
+            },
+            "specification": {
+                "@id": "codemeta:specification",
+                "@type": "@id"
+            },
+            "mediatorApplication": {
+                "@id": "codemeta:mediatorApplication",
+                "@type": "@id"
+            }
+        }
+    ],
+    "@type": "SoftwareSourceCode",
+    "identifier": "pyreduce-astro",
+    "name": "pyreduce-astro",
+    "version": "0.4b2+0.gffea46e.dirty",
+    "description": "A data reduction package for echelle spectrographs",
+    "license": "UNKNOWN, OSI Approved :: GNU General Public License v3 (GPLv3)",
+    "author": [{
+            "@type": "Person",
+            "givenName": "Ansgar",
+            "familyName": "Wehrhahn",
+            "email": "[email protected]"
+        },
+        {
+            "@type": "Person",
+            "givenName": "Nikolai",
+            "familyName": "Piskunov",
+            "email": "[email protected]"
+        }
+    ],
+    "provider": {
+        "@id": "https://pypi.org",
+        "@type": "Organization",
+        "name": "The Python Package Index",
+        "url": "https://pypi.org"
+    },
+    "runtimePlatform": "Python 3",
+    "url": "https://github.com/AWehrhahn/PyReduce",
+    "programmingLanguage": "Python 3",
+    "operatingSystem": "POSIX :: Linux",
+    "interfaceType": "LIB",
+    "contIntegration": "https://travis-ci.org/AWehrhahn/PyReduce"
+}

docs/Makefile

@@ -17,4 +17,4 @@ help:
 # Catch-all target: route all unknown targets to Sphinx using the new
 # "make mode" option.  $(O) is meant as a shortcut for $(SPHINXOPTS).
 %: Makefile
-	@$(SPHINXBUILD) -M $@ "$(SOURCEDIR)" "$(BUILDDIR)" $(SPHINXOPTS) $(O)
+	@$(SPHINXBUILD) -M $@ "$(SOURCEDIR)" "$(BUILDDIR)" $(SPHINXOPTS) $(O)

docs/conf.py

@@ -21,15 +21,16 @@
 
 
 # -- Project information -----------------------------------------------------
+from pyreduce import __version__
 
 project = "PyReduce"
 copyright = "2019, Ansgar Wehrhahn"
 author = "Ansgar Wehrhahn"
 
 # The short X.Y version
-version = ""
+version = __version__.split("+")[0]
 # The full version, including alpha/beta/rc tags
-release = "0.1"
+release = __version__
 
 
 # -- General configuration ---------------------------------------------------
@@ -82,7 +83,7 @@
 # The theme to use for HTML and HTML Help pages.  See the documentation for
 # a list of builtin themes.
 #
-html_theme = "alabaster"
+# html_theme = "alabaster"
 
 # Theme options are theme-specific and customize the look and feel of a theme
 # further.  For a list of options available for each theme, see the