Merge 6b2a99c into 17f68b0

.github/dependabot.yml

@@ -9,17 +9,14 @@ updates:
     directory: "/"
     schedule:
       interval: "monthly"
-    assignees:
-      - JoranAngevaare
+    open-pull-requests-limit: 5
   # Maintain the requirements requirements folder
   - package-ecosystem: "pip"
     directory: "/extra_requirements"
     schedule:
       # Check for updates to requirements every week
-      interval: "daily"
+      interval: "monthly"
     # Raise pull requests for version updates
     # to pip against the `develop` branch
     target-branch: "master"
-    open-pull-requests-limit: 15
-    assignees:
-      - JoranAngevaare
+    open-pull-requests-limit: 5

.github/workflows/pytest.yml

@@ -12,12 +12,13 @@ on:
 
 jobs:
   update:
-    name: "${{ matrix.test }}_py${{ matrix.python-version }}"
-    runs-on: ubuntu-latest
+    name: "${{matrix.os}} ${{ matrix.test }}_py${{ matrix.python-version }}"
+    runs-on: "${{ matrix.os }}"
     strategy:
       fail-fast: False
       matrix:
-        python-version: [ "3.8", "3.9", "3.10" ]
+        os:  ["ubuntu-latest" , "macos-latest" ]
+        python-version: [ "3.8", "3.9", "3.10", "3.11"]
         test: [ 'coveralls' ]
     env:
       NUMBA_DISABLE_JIT: 1
@@ -29,11 +30,17 @@ jobs:
           python-version: ${{ matrix.python-version }}
       - name: Checkout repo
         uses: actions/checkout@v3
-      - name: Install requirements
+      - name: Install latex (mac)
+        if: matrix.os == 'macos-latest'
+        run: brew install --cask basictex
+      - name: install latex (linux)
+        if: matrix.os == 'ubuntu-latest'
         run: |
           sudo apt-get update
           # sudo apt install texlive-full
           sudo apt install texlive texlive-latex-extra texlive-fonts-recommended dvipng cm-super
+      - name: install dependencies
+        run: |
           pip install -r extra_requirements/requirements-tests.txt
           python setup.py develop
       - name: Test package

README.md

@@ -1,7 +1,125 @@
 # ThesisPlots
 
-Collection of plots of dissertation thesis
+Collection of plots of dissertation thesis, simplified version of the [original repository](https://github.com/JoranAngevaare/thesis_plots)
 
-[![Coverage Status](https://coveralls.io/repos/github/JoranAngevaare/thesis_plots/badge.svg?branch=master)](https://coveralls.io/github/JoranAngevaare/thesis_plots?branch=master)
-[![CodeFactor](https://www.codefactor.io/repository/github/joranangevaare/thesis_plots/badge)](https://www.codefactor.io/repository/github/joranangevaare/thesis_plots)
+[![Coverage Status](https://coveralls.io/repos/github/XAMS-nikhef/thesis_plots/badge.svg?branch=master)](https://coveralls.io/github/XAMS-nikhef/thesis_plots?branch=master)
+[![CodeFactor](https://www.codefactor.io/repository/github/XAMS-nikhef/thesis_plots/badge)](https://www.codefactor.io/repository/github/XAMS-nikhef/thesis_plots)
 [![DOI](https://zenodo.org/badge/DOI/10.5281/zenodo.6527303.svg)](https://doi.org/10.5281/zenodo.6527303)
+
+
+## Use case
+If you want to organize your thesis plots in an easily reproducible manner, this might be a nice example for you.
+
+**Getting started**
+```
+# Clone the repository to your own github account, and copy it locally (or on a cluster)
+
+# clone the repository
+git clone git@github.com:<YOUR_GITHUB_ACCOUNT>/thesis_plots.git
+
+# install the repository and it's dependencies. You can either do this in your own or  
+pip install -e thesis_plots
+```
+
+Additionally, you want to setup latex such that you can use it to rended axis labels etc.
+There is an example in the [pytest](https://github.com/XAMS-nikhef/thesis_plots/blob/master/.github/workflows/pytest.yml) script for `linux` and
+`macos` (I'm sorry Windows users maybe you want to install a [WSL](https://learn.microsoft.com/en-us/windows/wsl/install) anyway 😉).
+The latex rendering on `macos` is still untested at the time of writing.
+
+
+Now you can add new notebooks in the notebooks folder.
+If you are happy with a new plot you made, you can upload it using the normal git commands:
+```
+cd thesis_plots
+
+# Check which changes you made
+git status
+git diff
+
+# Make a new branch
+git checkout -b <NEW_PROJECT>
+
+# Now add and commit to the repository
+git add <THE FILES YOU WANT TO ADD>
+git commit -m "<SOME DISCRIPTION>"
+git push --set-upstream origin <NEW_PROJECT>
+```
+This will crate a new branch on your repository which you can now view on you page `https://github.com/<YOUR_GITHUB_ACCOUNT>/thesis_plots`
+
+## Changing the setup
+In the file ``main.py`` you can customize the default style of plots that are set by the function `setup_plt`.
+The documentation on this is on [Matplotlib](https://matplotlib.org/stable/api/_as_gen/matplotlib.pyplot.rc.html).
+
+## Example usage
+Imagine that you made a new notebook with the following code in the notebook `notebooks/normal_distribution.ipynb`:
+```python
+import matplotlib.pyplot as plt
+import numpy as np
+from matplotlib.colors import LogNorm
+import thesis_plots
+distribution = np.random.normal(loc = 1, scale = 2, size = (2, 100_000))
+
+# Load your plotting style
+thesis_plots.setup_plt()
+
+# Make the plot
+plt.hist2d(*distribution, 
+           norm=LogNorm(), 
+           bins=25,
+           cmap='custom_map');
+plt.colorbar(label=thesis_plots.mathrm('Counts/bin'))
+plt.xlabel(thesis_plots.mathrm('X (some unit)'))
+plt.ylabel(thesis_plots.mathrm('Y (some unit)'))
+plt.title(thesis_plots.mathrm('Normal distribution'))
+```
+
+You can upload this notebook directly (following the commands above) or you can create a new module:
+```
+mkdir thesis_plots/normal_distribution
+touch thesis_plots/normal_distribution/normal_distribution_plot.py
+touch thesis_plots/normal_distribution/__init__.py
+```
+In `thesis_plots/__init__.py` you would add a line `from .normal_distribution import *`.
+In `touch thesis_plots/normal_distribution/__init__.py` you will import the `normal_distribution_plot.py` file similar to
+```python
+from . import normal_distribution_plot
+from .normal_distribution_plot import *
+```
+
+And in `thesis_plots/normal_distribution/normal_distribution_plot.py` you would make a function/class for the code you just wrote
+```python
+import matplotlib.pyplot as plt
+import numpy as np
+from matplotlib.colors import LogNorm
+import thesis_plots
+
+def plot_normal_distribution():
+    distribution = np.random.normal(loc = 1, scale = 2, size = (2, 100_000))
+
+    # Make the plot
+    plt.hist2d(*distribution, 
+               norm=LogNorm(), 
+               bins=25,
+               cmap='custom_map');
+    plt.colorbar(label=thesis_plots.mathrm('Counts/bin'))
+    plt.xlabel(thesis_plots.mathrm('X (some unit)'))
+    plt.ylabel(thesis_plots.mathrm('Y (some unit)'))
+    plt.title(thesis_plots.mathrm('Normal distribution'))
+```
+
+This greatly simplifies your notebook, where you can now reduce the code to:
+
+```python
+import thesis_plots
+# Load your plotting style
+thesis_plots.setup_plt()
+thesis_plots.normal_distribution.plot_normal_distribution()
+```
+
+## Advanced features
+ - Every time you make (or merge) a pull request, you will test making the plots on github actions. This prevents you 
+   from writing buggy code or forgetting to upload a data file.
+ - If you want to add data files, you can for instance do that in `data`, see the Lambda CDM example.
+ - You can setup a coverage report on `https://coveralls.io/github/<YOUR_GITHUB_USER>/thesis_plots` this allows you to view if all your code is actually used (and therefore useful)
+ - You can add tests in the `tests` folder, these are run as well when you commit to github.
+