docs: reform docs and add cocogitto mentions

.github/workflows/CI.yml

@@ -12,7 +12,7 @@ jobs:
       - uses: actions/checkout@v4
       - uses: conda-incubator/setup-miniconda@v3
         with:
-          activate-environment: scienv
+          activate-environment: goodsciproj_env
           environment-file: environment.yml
           auto-activate-base: false
 
@@ -25,7 +25,7 @@ jobs:
         run: |
           conda init
           source /home/runner/.bashrc
-          conda activate /usr/share/miniconda/envs/scienv
+          conda activate /usr/share/miniconda/envs/goodsciproj_env
           conda info --envs
 
       - name: Build Pybind11 module for C++ code
@@ -36,14 +36,14 @@ jobs:
         run: pytest ./tests
 
       - name: Install Doxygen
-        run: /usr/share/miniconda/envs/scienv/bin/doxygen --version
+        run: /usr/share/miniconda/envs/goodsciproj_env/bin/doxygen --version
         shell: bash
       - name: Generate Doxygen Documentation
         run: |
           cd docs &&
           mkdir build &&
           mkdir build/doxygen &&
-          /usr/share/miniconda/envs/scienv/bin/doxygen doxygen/doxygen.dox
+          /usr/share/miniconda/envs/goodsciproj_env/bin/doxygen doxygen/doxygen.dox
         shell: bash
 
       - name: Build docs

README.md

@@ -1,20 +1,20 @@
 # Template for Good Python and C++ Scientific Project
 
-This code is adapted from [this](https://juliadynamics.github.io/DrWatson.jl/stable) template for
+This code is adapted from [this template](https://juliadynamics.github.io/DrWatson.jl/stable) for
 Julia Language to make a reproducible scientific project for Python and C++ code in light of the
-guidelines from [this](https://www.youtube.com/watch?v=x3swaMSCcYk) Good Scientific Code Workshop by
+guidelines from [this Good Scientific Code Workshop](https://www.youtube.com/watch?v=x3swaMSCcYk) by
 George Datseris.
 
 ## Install
 To (locally) reproduce this project simply clone the repository:
 ```
 git clone https://github.com/yoctoyotta1024/GoodSciProjTemplate.git
 ```
-and then create an environment with the necessary dependencies installed (using micromamba, mamba
+and then create an environment with the necessary dependencies installed (e.g. using micromamba
 or conda as listed in the environment.yml):
 ```
-conda env create -f environment.yml
-conda activate scienv
+micromamba create -f environment.yml
+micromamba activate goodsciproj_env
 ```
 Finally you need to run ``pre-commit install`` but other than that everything should work out of
 the box and you can now run & have fun with the project... If not, please raise an issue on the

docs/source/index.rst

@@ -19,16 +19,18 @@ scientific practises into your GitHub repositories. The template demonstrates:
 
 * what to include in file headers
 * how to document your Python and C++ code
-* how to make tests for your code (using Python)
+* how to make tests for your code (using pytest)
 * how to liscence your code
-* how to make a citation for your code
-* things to include in .gitignore (e.g. large files like jupyter notebooks)
-* how to list the requirements of your code (i.e. dependencies) and make a Python environment .yml file
-* how to use pre-commit for code formatting (see https://pre-commit.com/)
-* how to use continuous integration (CI) to run your tests and publish your documentation on GitHub (see https://docs.github.com/en/actions/automating-builds-and-tests/about-continuous-integration)
+* how to write a citation for your code
+* things to include in a .gitignore file (e.g. large files like jupyter notebooks)
+* how to list the requirements of your code (i.e. dependencies) in an environment YAML file
+* how to use pre-commit for code checks, linting and formatting (see https://pre-commit.com/)
+* how to use continuous integration (CI) to run pytest and publish documentation on GitHub (see https://docs.github.com/en/actions/automating-builds-and-tests/about-continuous-integration)
+* how to write conventional commit messages
+* how to use conventional commits and CI for automatic version control on GitHub
 
 To (locally) reproduce this project, simply clone the repository. You will need to setup an
-environment with the dependencies installed and then run ``pre-commit install``, but other than
+environment with the dependencies installed and then run ``pre-commit install`` but other than
 that everything should work out of the box and you can now run & have fun with the project...
 If not, please raise an issue on the GitHub repository.
 

docs/source/usage/getstart.rst

@@ -9,13 +9,13 @@ Clone GoodSciProjTemplate's GitHub repository:
 
   $ git clone https://github.com/yoctoyotta1024/GoodSciProjTemplate.git
 
-and then create an environment with the necessary dependencies installed (using micromamba, mamba
+and then create an environment with the necessary dependencies installed (e.g. using micromamba,
 or conda as listed in the environment.yml):
 
 .. code-block:: console
 
-  $ micromamba env create -f environment.yml
-  $ micromamba activate scienv
+  $ micromamba create -f environment.yml
+  $ micromamba activate goodsciproj_env
 
 Finally install the pre-commit hooks:
 
@@ -29,6 +29,9 @@ more about the powers of pre-commit from `their documentation: <https://pre-comm
 That's it, you're done! But maybe now you want to customise the project and push it to your own
 GitHub repo...
 
+Making the Project Your Own
+===========================
+
 Necessary first steps:
 ###########################
 
@@ -46,6 +49,8 @@ Necessary second steps:
 #. Corect the repository name and its owner for GitHub (e.g. in the CI.yml and cog.toml).
 #. Write a new README.md (shorter is generally better) and include a link to your documentation in it.
 #. Change the GitHub links in the .rst files to the correct ones for your GitHub repository (*hint*: you find these files in the `docs` directory).
+#. Setup (or delete) cocogitto
+#. Setup (or delete) Python bindings for C++
 
 Some suggested third steps:
 ###########################
@@ -62,7 +67,8 @@ Want more ideas?!
 #################
 Have you thought about adding contributors, acknowledgements, more Python and/or
 other requirements/enviroments, more CI or pre-commit tasks, and an automatic file header
-generator? Maybe you've noticed the repo uses  `conventional commit<https://www.conventionalcommits.org/en/v1.0.0/>`_
+generator? Maybe you've noticed this repository uses 
+`conventional commit <https://www.conventionalcommits.org/en/v1.0.0/>`_
 messages to enable `cocogitto<https://docs.cocogitto.io/>`_'s automatic version control?
 Or maybe you should ponder all this over a cup of tea and some biscuits...
 

environment.yml

@@ -1,4 +1,4 @@
-name: scienv
+name: goodsciproj_env
 dependencies:
     - python>=3.9
     - pytest