Change package layout / modernize installation

.github/workflows/ci.yml

@@ -0,0 +1,38 @@
+name: ci
+
+on: [push, pull_request]
+
+jobs:
+  build:
+
+    runs-on: ubuntu-latest
+    strategy:
+      matrix:
+        python-version: ["3.9", "3.10", "3.11"]
+
+    steps:
+      - name: Checkout
+        uses: actions/checkout@v4
+        with:
+          fetch-depth: 0
+
+      - name: Set up Python ${{ matrix.python-version }}
+        uses: actions/setup-python@v4
+        with:
+          python-version: ${{ matrix.python-version }}
+
+      - name: Install dependencies
+        run: |
+          python -m pip install --upgrade pip
+          pip install ".[test]"
+
+      - 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 tests

.github/workflows/docs.yml

@@ -0,0 +1,56 @@
+name: sphinxdocumentation
+
+on: [push]
+
+jobs:
+  build:
+
+    runs-on: ubuntu-latest
+
+    steps:  
+    - name: Checkout code
+      uses: actions/checkout@v4
+      with:
+        fetch-depth: 0 
+
+    - name: Set up Python 
+      uses: actions/setup-python@v4
+      with:
+        python-version: "3.11"
+
+
+    - name: Install docs dependencies
+      run: |
+        pip install --upgrade pip
+        pip install -e ".[docs]"
+
+    - name: Build docs
+      working-directory: ./docs
+      run: |
+        make html
+#      uses: ammaraskar/sphinx-action@master
+#      with:
+#        docs-folder: "docs/"
+
+    # Publish built docs to gh-pages branch.
+    # ===============================
+    - name: Commit documentation changes
+      run: |
+        git clone https://github.com/ammaraskar/sphinx-action-test.git --branch gh-pages --single-branch gh-pages
+        cp -r docs/_build/html/* gh-pages/
+        cd gh-pages
+        touch .nojekyll
+        git config --local user.email "[email protected]"
+        git config --local user.name "GitHub Action"
+        git add .
+        git commit -m "Update documentation" -a || true
+        # The above command will fail if no changes were present, so we ignore
+        # that.
+    - name: Push changes
+      uses: ad-m/github-push-action@master
+      with:
+        branch: gh-pages
+        directory: gh-pages
+        github_token: ${{ secrets.GITHUB_TOKEN }}
+        force: true
+    # ===============================

.gitignore

@@ -1,3 +1,4 @@
+.DS_Store
 # Byte-compiled / optimized / DLL files
 __pycache__/
 *.py[cod]
@@ -26,6 +27,7 @@ share/python-wheels/
 .installed.cfg
 *.egg
 MANIFEST
+*_version.py
 
 # PyInstaller
 #  Usually these files are written by a python script from a template
@@ -70,6 +72,7 @@ instance/
 
 # Sphinx documentation
 docs/_build/
+docs/api/
 
 # PyBuilder
 target/

README.rst

@@ -7,13 +7,15 @@ TRAP is novel algorithm used to detect exoplanets in high-contrast imaging data,
 in the time-domain. The main benefit of this new approach is that it works significantly better for companion signals very close to the central star.
 For a detailed description please refer to `Samland et al. 2021 <https://ui.adsabs.harvard.edu/abs/2021A%26A...646A..24S/abstract>`_.
 
-TRAP can currently only be installed from source and requires at least Python 3.5 or higher. We recommend using the "pip install" or "pip install -e ." command (if you want to make changes to the code base) in the directory containing the "setup.py" file.
-TRAP is using Ray for multiprocessing, we recommend installing it via 'pip install -U "ray[default]"' to get access to the dashboard for monitoring utilities.
+TRAP requires at least Python 3.8 or higher (3.12 will be supported soon). The latest version can be installed using "pip install git+https://github.com/m-samland/trap/".
+If the user wishes to contribute or change the code, we recommend cloning the repository and using the "pip install -e ." command.
+
+TRAP is using Ray for multiprocessing. If you are using a cluster, please make sure that Ray is installed on the cluster as well.
 
 The package has been tested on Linux/iOS/Windows with the packages provided in any recent version of Conda.
 Please provide feedback if there are issues installing the package on your system.
 
-A detailed documentation website is not available at the moment. Please refer to the in-code documentation and the tutorial notebook containing a simple example based on the test data included in the package.
+Please make use of the tutorial notebook in the examples folder explaining how to use TRAP. The folder also contains data from the VLT/SPHERE instrument needed for the tutorial.
 
 Dependencies
 ------------

docs/Makefile

@@ -0,0 +1,20 @@
+# Minimal makefile for Sphinx documentation
+#
+
+# You can set these variables from the command line, and also
+# from the environment for the first two.
+SPHINXOPTS    ?=
+SPHINXBUILD   ?= sphinx-build
+SOURCEDIR     = .
+BUILDDIR      = _build
+
+# Put it first so that "make" without argument is like "make help".
+help:
+	@$(SPHINXBUILD) -M help "$(SOURCEDIR)" "$(BUILDDIR)" $(SPHINXOPTS) $(O)
+
+.PHONY: help Makefile
+
+# 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)

docs/conf.py

@@ -0,0 +1,53 @@
+# Configuration file for the Sphinx documentation builder.
+#
+# This file only contains a selection of the most common options. For a full
+# list see the documentation:
+# https://www.sphinx-doc.org/en/master/usage/configuration.html
+
+# -- Path setup --------------------------------------------------------------
+
+# If extensions (or modules to document with autodoc) are in another directory,
+# add these directories to sys.path here. If the directory is relative to the
+# documentation root, use os.path.abspath to make it absolute, like shown here.
+#
+# import os
+# import sys
+# sys.path.insert(0, os.path.abspath('.'))
+
+
+# -- Project information -----------------------------------------------------
+
+project = 'my_package'
+copyright = '2022, Author Name'
+author = 'Author Name'
+
+
+# -- General configuration ---------------------------------------------------
+
+# Add any Sphinx extension module names here, as strings. They can be
+# extensions coming with Sphinx (named 'sphinx.ext.*') or your custom
+# ones.
+extensions = ['sphinx_automodapi.automodapi'
+]
+numpydoc_show_class_members = False
+
+# Add any paths that contain templates here, relative to this directory.
+templates_path = ['_templates']
+
+# List of patterns, relative to source directory, that match files and
+# directories to ignore when looking for source files.
+# This pattern also affects html_static_path and html_extra_path.
+exclude_patterns = ['_build', 'Thumbs.db', '.DS_Store']
+
+
+# -- Options for HTML output -------------------------------------------------
+
+# The theme to use for HTML and HTML Help pages.  See the documentation for
+# a list of builtin themes.
+#
+html_theme = 'alabaster'
+
+# Add any paths that contain custom static files (such as style sheets) here,
+# relative to this directory. They are copied after the builtin static files,
+# so a file named "default.css" will overwrite the builtin "default.css".
+html_static_path = ['_static']

docs/index.rst

@@ -0,0 +1,67 @@
+.. my_package documentation master file, created by
+   sphinx-quickstart on Tue Mar 22 13:13:41 2022.
+   You can adapt this file completely to your liking, but it should at least
+   contain the root `toctree` directive.
+
+Welcome to my_package's documentation!
+======================================
+
+.. toctree::
+   :maxdepth: 2
+   :caption: Contents:
+
+
+Here is where you can write the documentation for your package. 
+
+
+Usage
+=====
+
+.. _installation:
+
+Installation
+------------
+
+To use `my_package` you need to install X, Y and Z. 
+
+
+.. _code:
+
+Code
+----
+
+Here is an example of describing the use of your function.
+
+To add one to a number you can use the ``my_package.add_one()`` function:
+
+.. py:function:: my_package.add_one(number)
+
+
+    :param number: Should be integer, floating point number or a string. 
+
+    If ``number`` is not one of these types, an exception will be raised:
+
+    .. py:exception:: TypeError
+
+   Raised if the input is invalid.
+
+More about how to describe code can be hound 
+`here <https://www.sphinx-doc.org/en/master/tutorial/describing-code.html>`_
+
+
+..
+  The following section creates an index, a list of modules and a 
+  search page. 
+
+Indices and tables
+==================
+
+* :ref:`genindex`
+* :ref:`modindex`
+* :ref:`search`
+
+..
+ The following will add the signature of the individual functions and pull
+ their docstrings.
+
+.. automodapi:: my_package.example

docs/make.bat

@@ -0,0 +1,35 @@
+@ECHO OFF
+
+pushd %~dp0
+
+REM Command file for Sphinx documentation
+
+if "%SPHINXBUILD%" == "" (
+	set SPHINXBUILD=sphinx-build
+)
+set SOURCEDIR=.
+set BUILDDIR=_build
+
+if "%1" == "" goto help
+
+%SPHINXBUILD% >NUL 2>NUL
+if errorlevel 9009 (
+	echo.
+	echo.The 'sphinx-build' command was not found. Make sure you have Sphinx
+	echo.installed, then set the SPHINXBUILD environment variable to point
+	echo.to the full path of the 'sphinx-build' executable. Alternatively you
+	echo.may add the Sphinx directory to PATH.
+	echo.
+	echo.If you don't have Sphinx installed, grab it from
+	echo.https://www.sphinx-doc.org/
+	exit /b 1
+)
+
+%SPHINXBUILD% -M %1 %SOURCEDIR% %BUILDDIR% %SPHINXOPTS% %O%
+goto end
+
+:help
+%SPHINXBUILD% -M help %SOURCEDIR% %BUILDDIR% %SPHINXOPTS% %O%
+
+:end
+popd