Merge pull request #5 from richardkoehler/0.2.0

0.2.0

.github/workflows/tests.yml

@@ -29,7 +29,6 @@ jobs:
           - {name: 3.10 Linux, python: '3.10', os: ubuntu-latest, tox: py310}
           - {name: 3.10 Windows, python: '3.10', os: windows-latest, tox: py310}
           - {name: 3.10 Mac, python: '3.10', os: macos-latest, tox: py310}
-          - {name: 3.9 Linux, python: '3.9', os: ubuntu-latest, tox: py39}
           - {name: Lint, python: '3.10', os: ubuntu-latest, tox: lint}
           - {name: Typing, python: '3.10', os: ubuntu-latest, tox: typing}
           - {name: Style, python: '3.10', os: ubuntu-latest, tox: style}

.gitignore

@@ -1,5 +1,5 @@
 # Byte-compiled / optimized / DLL files
-__pycache__/
+*__pycache__
 *.py[cod]
 *$py.class
 

README.md

@@ -32,10 +32,17 @@ To install the latest delevopment version, first clone this repository:
 $ git clone https://github.com/richardkoehler/pte-stats
 ```
 
-Then install with the command:
+If you are using conda, simply run:
 
 ```bash
-$ pip install .
+$ conda env create -f env.yml
+$ conda activate pte-stats
+```
+
+If you want to install pte-stats into an existing environment, type:
+
+```bash
+$ pip install -e .
 ```
 
 
@@ -56,9 +63,16 @@ For any minor additions or bugfixes, you may simply create a **pull request**.
 For any major changes, make sure to open an **issue** first. When you then create a pull request, be sure to **link the pull request** to the open issue in order to close the issue automatically after merging.
 
 ### How to contribute
-To contribute yourselves, you should fork this repository, and create your a development branch from your fork.
+To contribute yourselves, you should fork this repository, and then create a development branch from your fork.
+
+Then, inside your development branch run the commands:
+
+```bash
+$ conda env create -f env_dev.yml
+$ conda activate pte-stats-dev
+```
 
-Then, inside your development branch run the command:
+... or simply:
 
 ```bash
 $ pip install -e .[dev]
@@ -71,17 +85,17 @@ PTE Stats is licensed under the [MIT license](license-url).
 
 <!-- MARKDOWN LINKS & IMAGES -->
 <!-- https://www.markdownguide.org/basic-syntax/#reference-style-links -->
-[python-shield]: https://img.shields.io/static/v1?label=Python&message=3.9|3.10&logoColor=black&labelColor=grey&color=blue
+[python-shield]: https://img.shields.io/static/v1?label=Python&message=3.10&logoColor=black&labelColor=grey&color=blue
 [python-url]: https://pypi.org/project/pte-stats/
-[pypi-shield]: https://img.shields.io/static/v1?label=PyPi&message=v0.1.0&logoColor=black&labelColor=grey&color=blue
+[pypi-shield]: https://img.shields.io/static/v1?label=PyPi&message=v0.2.0&logoColor=black&labelColor=grey&color=blue
 [pypi-url]: https://pypi.org/project/pte-stats/
 [tests-shield]: https://github.com/richardkoehler/pte-stats/actions/workflows/tests.yml/badge.svg
 [tests-url]: https://github.com/richardkoehler/pte-stats/actions/workflows/tests.yml
-[homepage-shield]: https://img.shields.io/static/v1?label=Homepage&message=ICN&logoColor=black&labelColor=grey&logoWidth=20&color=9cf
+[homepage-shield]: https://img.shields.io/static/v1?label=Homepage&message=ICN&logoColor=black&labelColor=grey&color=9cf
 [homepage-url]: https://www.icneuromodulation.org/
 [contributors-shield]: https://img.shields.io/github/contributors/richardkoehler/pte-stats.svg
 [contributors-url]: https://github.com/richardkoehler/pte-stats/graphs/contributors
-[license-shield]: https://img.shields.io/static/v1?label=License&message=MIT&logoColor=black&labelColor=grey&logoWidth=20&color=yellow
+[license-shield]: https://img.shields.io/static/v1?label=License&message=MIT&logoColor=black&labelColor=grey&color=yellow
 [license-url]: https://github.com/richardkoehler/pte-stats/blob/main/LICENSE/
-[codestyle-shield]: https://img.shields.io/static/v1?label=CodeStyle&message=black&logoColor=black&labelColor=grey&logoWidth=20&color=black
+[codestyle-shield]: https://img.shields.io/static/v1?label=CodeStyle&message=black&logoColor=black&labelColor=grey&color=black
 [codestyle-url]: https://github.com/psf/black

env.yml

@@ -1,13 +1,8 @@
 name: pte-stats
 channels:
-  - conda-forge
   - defaults
 dependencies:
-  - joblib
-  - numba
-  - numpy
   - pip
-  - python>=3.9
-  - scikit-image
-  - statsmodels
-
+  - python=3.10
+  - pip:
+    - -e .

env_dev.yml

@@ -2,20 +2,8 @@ name: pte-stats-dev
 channels:
   - defaults
 dependencies:
-  - python>=3.9
   - pip
+  - python=3.10
   - pip:
-    # basic dependencies
-    - joblib
-    - numba
-    - numpy
-    - scikit-image
-    - statsmodels
-    # development dependencies
-    - black
-    - isort
-    - mypy
-    - pylint
-    - pytest
-    - pytest-cov
+    - -e .[dev]
 

pyproject.toml

@@ -4,46 +4,42 @@ requires = ["flit_core >=3.5,<4"]
 
 [project]
 authors = [
-  {name = "Richard Koehler"},
+  {name = "Richard M. Köhler"},
 ]
 classifiers = [
   "Development Status :: 2 - Pre-Alpha",
   "License :: OSI Approved :: MIT License",
-  "Programming Language :: Python :: 3.9",
-  "Programming Language :: Python :: 3.10",
+  "Programming Language :: Python",
   "Topic :: Software Development :: Libraries :: Python Modules",
 ]
 description = "An open-source software package for statistics with time series."
 dynamic = ["version"]
 keywords = ["statistics", "timeseries", "eeg", "ieeg"]
-license = {file = "LICENSE.txt"}
+license = {file = "LICENSE"}
 maintainers = [
-  {name = "Richard Koehler"},
+  {name = "Richard M. Köhler"},
 ]
 name = "pte-stats"
 readme = {file = "README.md", content-type = "text/markdown"}
-requires-python = ">=3.9"
+requires-python = ">=3.10"
 
 dependencies = [
-  "joblib",
   "numba",
   "numpy",
-  "pip",
   "scikit-image",
   "statsmodels",
 ]
 
 [project.optional-dependencies]
-deploy = [
-  "flit",
-]
 dev = [
   "black",
   "isort",
   "mypy",
+  "pip-tools",
   "pylint",
   "pytest",
   "pytest-cov",
+  "tox",
 ]
 
 [tool.flit.module]
@@ -63,7 +59,7 @@ exclude = '''
 include = '''
 (
     /tests
-  | src/pte_stats/
+  | /src/
 )
 '''
 line-length = 79

requirements/requirements.in

@@ -0,0 +1,4 @@
+  numba
+  numpy
+  scikit-image
+  statsmodels

requirements/requirements.txt

@@ -1,19 +1,63 @@
-imageio==2.14.1
-joblib==1.1.0
+#
+# This file is autogenerated by pip-compile with python 3.10
+# To update, run:
+#
+#    pip-compile requirements.in
+#
+imageio==2.16.2
+    # via scikit-image
 llvmlite==0.38.0
-networkx==2.6.3
+    # via numba
+networkx==2.8
+    # via scikit-image
 numba==0.55.1
-numpy==1.21.5
+    # via -r requirements.in
+numpy==1.21.6
+    # via
+    #   -r requirements.in
+    #   imageio
+    #   numba
+    #   pandas
+    #   patsy
+    #   pywavelets
+    #   scikit-image
+    #   scipy
+    #   statsmodels
+    #   tifffile
 packaging==21.3
-pandas==1.4.0
+    # via
+    #   scikit-image
+    #   statsmodels
+pandas==1.4.2
+    # via statsmodels
 patsy==0.5.2
-Pillow==9.0.1
-pyparsing==3.0.7
+    # via statsmodels
+pillow==9.1.0
+    # via
+    #   imageio
+    #   scikit-image
+pyparsing==3.0.8
+    # via packaging
 python-dateutil==2.8.2
-pytz==2021.3
-PyWavelets==1.2.0
-scikit-image==0.19.1
-scipy==1.7.3
+    # via pandas
+pytz==2022.1
+    # via pandas
+pywavelets==1.3.0
+    # via scikit-image
+scikit-image==0.19.2
+    # via -r requirements.in
+scipy==1.8.0
+    # via
+    #   scikit-image
+    #   statsmodels
 six==1.16.0
-statsmodels==0.13.1
-tifffile==2021.11.2
+    # via
+    #   patsy
+    #   python-dateutil
+statsmodels==0.13.2
+    # via -r requirements.in
+tifffile==2022.4.8
+    # via scikit-image
+
+# The following packages are considered to be unsafe in a requirements file:
+# setuptools

requirements/requirements_backup.txt

@@ -0,0 +1,62 @@
+#
+# This file is autogenerated by pip-compile with python 3.10
+# To update, run:
+#
+#    pip-compile requirements.in
+#
+imageio==2.14.1
+    # via scikit-image
+llvmlite==0.38.0
+    # via numba
+networkx==2.6.3
+    # via scikit-image
+numba==0.55.1
+    # via -r requirements.in
+numpy==1.21.5
+    # via
+    #   -r requirements.in
+    #   imageio
+    #   numba
+    #   pandas
+    #   patsy
+    #   pywavelets
+    #   scikit-image
+    #   scipy
+    #   statsmodels
+    #   tifffile
+packaging==21.3
+    # via scikit-image
+pandas==1.4.0
+    # via statsmodels
+patsy==0.5.2
+    # via statsmodels
+pillow==9.0.1
+    # via
+    #   imageio
+    #   scikit-image
+pyparsing==3.0.7
+    # via packaging
+python-dateutil==2.8.2
+    # via pandas
+pytz==2021.3
+    # via pandas
+pywavelets==1.2.0
+    # via scikit-image
+scikit-image==0.19.1
+    # via -r requirements.in
+scipy==1.7.3
+    # via
+    #   scikit-image
+    #   statsmodels
+six==1.16.0
+    # via
+    #   patsy
+    #   python-dateutil
+statsmodels==0.13.1
+    # via -r requirements.in
+tifffile==2021.11.2
+    # via scikit-image
+
+# The following packages are considered to be unsafe in a requirements file:
+# pip
+# setuptools

requirements/requirements_deploy.in

@@ -0,0 +1,3 @@
+-c requirements.txt
+-c requirements_dev.txt
+flit