Dev

.github/workflows/draft-pdf.yml

@@ -1,4 +1,10 @@
-on: [push]
+on:
+  push:
+    branches-ignore:
+      #cannot be ran on protected branches
+      - 'main' 
+      - 'dev'
+      - 'gh-pages'
 
 jobs:
   paper:

.github/workflows/main_workflow.yml

@@ -225,8 +225,8 @@ jobs:
             force_orphan: true
 
 
-#---- Deploy documentation -----#
-   deploy_doc:
+#---- Deploy documentation MAIN-----#
+   deploy_doc_main:
     name: Deploy main documentation
     needs: [doctests,run-tests,versiontest,mac_install_testing, windows_install_testing]
     runs-on: ubuntu-latest
@@ -270,11 +270,58 @@ jobs:
             publish_dir: _build/
             force_orphan: true
 
+#---- Deploy documentation dev -----#
+   deploy_doc_dev:
+    name: Deploy Dev documentation
+    needs: [doctests,run-tests,versiontest,mac_install_testing, windows_install_testing]
+    runs-on: ubuntu-latest
+    if: |
+        github.ref == 'refs/heads/dev'
+    steps:
+        - uses: actions/checkout@v3
+        - name: Set up Python39
+          uses: actions/setup-python@v4
+          with:
+            python-version: '3.9'
+            #cache: 'poetry'
+        # You can test your matrix by printing the current Python version
+        - name: Display Python version
+          run: python -c "import sys; print(sys.version)"
+        - name: install pandoc (system wide)
+          run: |
+              sudo apt-get -y install pandoc
+        - name: Download the package build
+          uses: actions/download-artifact@v3
+          with:
+            name: package_build
+        - name: Install the package
+          run: |
+              python3 -m pip install ./metobs_toolkit-*.tar.gz
+        - name: get documentation requirements
+          uses: actions/download-artifact@v3
+          with:
+            name: documentation_requirements
+        - name: install doc depending packages
+          run: |
+              pip install -r only_doc_req.txt
+        - name: Build documentation
+          run: |
+              sphinx-build -a -E docs _build
+        - name: deploy documentation
+          uses: peaceiris/actions-gh-pages@v3
+          with:
+            publish_branch: gh-pages-dev
+            github_token: ${{ secrets.GITHUB_TOKEN }}
+            publish_dir: _build/
+            force_orphan: true
+
+
+
 
 # ---- delete artifacts that are not for storage -----
    cleanup_artifacts:
      name: delete artifacts
-     needs: [doctests,run-tests,versiontest,mac_install_testing, windows_install_testing, deploy_doc]
+     needs: [doctests,run-tests,versiontest,mac_install_testing, windows_install_testing, deploy_doc_main]
      runs-on: ubuntu-latest
      steps:
      - uses: actions/checkout@v3
@@ -284,4 +331,3 @@ jobs:
              package_build
              documentation_requirements
              titan_requirements
-

.gitignore

@@ -22,19 +22,21 @@ docs/examples/*.py
 
 #Exclude local documentation builds
 docs/_*
+!docs/_build
 
 #logs
 *log
 #exclude data
-examples/*.csv
-examples/testdata.csv
+fairness_demo_exercises/*.csv
+fairness_demo_exercises/testdata.csv
 tests/test_data/testdata_testday
 # exclued logs
 *log
 
 #exclude figures in test data
-tests/**/*.png
-tests/**/*.html
+tests/*.png
+tests/*.html
+
 
 # pychache
 *.ipynb_checkpoints*
@@ -51,4 +53,4 @@ GUI/cache/*
 #Development stuff
 development/*
 #Documentation (build online)
-docs/_build
+#docs/_build

.pre-commit-config.yaml

@@ -0,0 +1,31 @@
+repos:
+-   repo: https://github.com/pre-commit/pre-commit-hooks
+    rev: v4.4.0
+    hooks:
+    -   id: check-yaml
+    -   id: check-toml
+    -   id: end-of-file-fixer
+    -   id: trailing-whitespace
+-   repo: https://github.com/psf/black
+    rev: 22.10.0
+    hooks:
+    -   id: black
+- repo: https://github.com/macisamuele/language-formatters-pre-commit-hooks
+  rev: v2.12.0
+  hooks:
+  - id: pretty-format-toml
+    args: [--autofix]
+
+#- repo: https://github.com/pycqa/flake8
+#  rev: 6.1.0
+#  hooks:
+#  - id: flake8
+#    additional_dependencies: ['flake8-alphabetize', 'flake8-rst-docstrings']
+#    args: ['--config=setup.cfg']
+
+ci:
+  autofix_commit_msg: |
+    [pre-commit.ci] auto fixes from pre-commit.com hooks
+
+    for more information, see https://pre-commit.ci
+  autofix_prs: true

.readthedocs.yaml

@@ -6,7 +6,7 @@ version: 2
 
 # Set the version of Python and other tools you might need
 build:
-  os: ubuntu-20.04
+  os: ubuntu-22.04
   tools: {python: "3.10"}
   jobs:
     pre_create_environment:
@@ -21,4 +21,4 @@ build:
 # Build documentation in the docs/ directory with Sphinx
 sphinx:
   configuration: docs/conf.py
-  fail_on_warning: true
+  fail_on_warning: true

CONTRIBUTING.md

@@ -92,7 +92,7 @@ Make sure you have this software installed before proceeding.
   git checkout name-of-your-bugfix-or-feature
   ```
  Now you can make local changes.
- 
+
 4. Test your changes locally. The [build_and_test.sh](https://github.com/vergauwenthomas/MetObs_toolkit/blob/master/deploiment/build_and_test.sh) script builds the package and runs a series of tests. All tests must be successful before your contributions can be merged in the dev branch.
 
   ```
@@ -126,4 +126,4 @@ After the code review, and all review marks are resolved, your contributions wil
 For general support or questions, you can refer them to @vergauwenthomas, or by mail to ([email protected]).
 
 ## Acknowledgement
-This file is inspired by the [RavenPy](https://github.com/CSHS-CWRA/RavenPy) project. Thank you for the inspiration!”. 
+This file is inspired by the [RavenPy](https://github.com/CSHS-CWRA/RavenPy) project. Thank you for the inspiration!”.

LICENSE

@@ -1,5 +1,6 @@
 Copyright (c) 2023 Atmospheric Physics group Ghent University
 
+
 Permission is hereby granted, free of charge, to any person obtaining a copy
 of this software and associated documentation files (the "Software"), to deal
 in the Software without restriction, including without limitation the rights

README.md

@@ -10,6 +10,7 @@
 
 
 The MetObs-toolkit provides a comprehensive framework for scientists to process raw meteorological data for analysis.
+
 This repo contains all the software for the [metobs_toolkit](https://test.pypi.org/project/metobs-toolkit/).
 
 ## Documentation
@@ -19,7 +20,7 @@ Documentation can be found [here](https://vergauwenthomas.github.io/MetObs_toolk
 ## Installing the package
 Install the package using pip:
 
-```bash 
+```bash
 pip3 install metobs-toolkit
  ```
 To install the PyPi version of the toolkit. To install the github versions one can use these commands:
@@ -43,21 +44,21 @@ pip3 install metobs-toolkit titanlib
 To use the package, import it in Python:
 
 
-```python 
+```python
 import metobs_toolkit
 
 #Check your version
 metobs_toolkit.__version__
  ```
 ## Exercises and demos
-In the context of a [FAIRNESS (COST action)](https://www.fairness-ca20108.eu/) summer school, a set of well-documented exercises and demos are made. 
+In the context of a [FAIRNESS (COST action)](https://www.fairness-ca20108.eu/) summer school, a set of well-documented exercises and demos are made.
 
 | Notebook  | Description  |       |
 |:----------|:-------------|------:|
-| [Introduction](https://github.com/vergauwenthomas/MetObs_toolkit/blob/master/examples/Introduction_01.ipynb) | Introduction to the toolkit | [![Open In Colab](https://colab.research.google.com/assets/colab-badge.svg)](https://colab.research.google.com/github/vergauwenthomas/MetObs_toolkit/blob/master/examples/Introduction_01.ipynb) |
-| [Quality control](https://github.com/vergauwenthomas/MetObs_toolkit/blob/master/examples/Quality_control_excercise_02.ipynb) | Introduction to quality control methods | [![Open In Colab](https://colab.research.google.com/assets/colab-badge.svg)](https://colab.research.google.com/github/vergauwenthomas/MetObs_toolkit/blob/master/examples/Quality_control_excercise_02.ipynb)|
-| [Filling gaps](https://github.com/vergauwenthomas/MetObs_toolkit/blob/master/examples/Gap_filling_excercise_03.ipynb) | Introduction to gap filling methods | [![Open In Colab](https://colab.research.google.com/assets/colab-badge.svg)](https://colab.research.google.com/github/vergauwenthomas/MetObs_toolkit/blob/master/examples/Gap_filling_excercise_03.ipynb)|
-| [Analysis](https://github.com/vergauwenthomas/MetObs_toolkit/blob/master/examples/Urban_analysis_excercise_04.ipynb) | Introduction analysis methods | [![Open In Colab](https://colab.research.google.com/assets/colab-badge.svg)](https://colab.research.google.com/github/vergauwenthomas/MetObs_toolkit/blob/master/examples/Urban_analysis_excercise_04.ipynb)|
+| [Introduction](https://github.com/vergauwenthomas/MetObs_toolkit/blob/master/fairness_demo_exercises/Introduction_01.ipynb) | Introduction to the toolkit | [![Open In Colab](https://colab.research.google.com/assets/colab-badge.svg)](https://colab.research.google.com/github/vergauwenthomas/MetObs_toolkit/blob/master/fairness_demo_exercises/Introduction_01.ipynb) |
+| [Quality control](https://github.com/vergauwenthomas/MetObs_toolkit/blob/master/fairness_demo_exercises/Quality_control_excercise_02.ipynb) | Introduction to quality control methods | [![Open In Colab](https://colab.research.google.com/assets/colab-badge.svg)](https://colab.research.google.com/github/vergauwenthomas/MetObs_toolkit/blob/master/fairness_demo_exercises/Quality_control_excercise_02.ipynb)|
+| [Filling gaps](https://github.com/vergauwenthomas/MetObs_toolkit/blob/master/fairness_demo_exercises/Gap_filling_excercise_03.ipynb) | Introduction to gap filling methods | [![Open In Colab](https://colab.research.google.com/assets/colab-badge.svg)](https://colab.research.google.com/github/vergauwenthomas/MetObs_toolkit/blob/master/fairness_demo_exercises/Gap_filling_excercise_03.ipynb)|
+| [Analysis](https://github.com/vergauwenthomas/MetObs_toolkit/blob/master/fairness_demo_exercises/Urban_analysis_excercise_04.ipynb) | Introduction analysis methods | [![Open In Colab](https://colab.research.google.com/assets/colab-badge.svg)](https://colab.research.google.com/github/vergauwenthomas/MetObs_toolkit/blob/master/fairness_demo_exercises/Urban_analysis_excercise_04.ipynb)|
 
 
 ## Related

deploiment/build_and_test.sh

@@ -19,7 +19,8 @@ DOCEXAMPLEDIR=${WORKDIR}/docs/examples
 #1 install the package using poetry
 
 poetry update #to update the poetry.lock with the latest versions of the depending packages
-poetry install --with documentation,dev,titan
+poetry install --all-extras
+
 
 
 #list all packages installed (for debugging)

docs/MetObs_documentation.rst

@@ -14,4 +14,4 @@ the MetObs toolkit to be used by a user.
    metobs_toolkit.dataset
    metobs_toolkit.station
    metobs_toolkit.analysis
-   metobs_toolkit.modeldata
+   metobs_toolkit.modeldata

docs/_build/.buildinfo

@@ -0,0 +1,4 @@
+# Sphinx build info version 1
+# This file hashes the configuration used when building these files. When it is not found, a full rebuild will be done.
+config: 1dde347d84ddc46cb70aec8f405101e4
+tags: 645f666f9bcd5a90fca523b33c5a78b7