Setup enhancements

.pre-commit-config.yaml

@@ -0,0 +1,29 @@
+repos:
+  - repo: https://github.com/pre-commit/pre-commit-hooks
+    rev: v5.0.0
+    hooks:
+      - id: trailing-whitespace
+      - id: end-of-file-fixer
+      - id: check-yaml
+      - id: check-added-large-files
+      - id: check-ast
+      - id: check-docstring-first
+      - id: check-json
+      - id: pretty-format-json
+        args: ['--autofix']
+      - id: check-toml
+      - id: mixed-line-ending
+        args: ['--fix', 'auto']
+      - id: name-tests-test
+        args: ['--pytest-test-first']
+      - id: requirements-txt-fixer
+  - repo: https://github.com/Lucas-C/pre-commit-hooks
+    rev: v1.5.5
+    hooks:
+      - id: remove-tabs
+  - repo: https://github.com/astral-sh/ruff-pre-commit
+    rev: v0.11.8
+    hooks:
+      - id: ruff
+        args: [ --fix ]
+      - id: ruff-format

README.md

@@ -22,59 +22,78 @@ git clone --recursive https://github.com/NationalGenomicsInfrastructure/genomics
 
 <details>
 
-<summary>Note on `conda` environments</summary>
+<summary>Note on MacOS installations</summary>
 
-#### Create the environment with the correct dependencies
+### Fix library issues
 
-If you decide to use a conda environment, create one making sure to use the `conda_requirements.yml` file with the following command:
+If you are using MacOS, you might run into some issues with the libraries when running the app. 
+
+In case you get the `OSError: cannot load library 'gobject-2.0-0'` error (or similar), install `glib` and `pango` via [Homebrew](https://brew.sh/):
 
 ```bash
-conda env create -n <env_name> -f conda_requirements.yml
+brew install glib
+brew install pango
 ```
 
-where `<env_name>` is the name of the environment you want to create.  Then, activate the environment with:
+and then symlink the libraries to `/usr/local/lib`:
 
 ```bash
-conda activate <env_name>
+sudo ln -s /opt/homebrew/opt/glib/lib/libgobject-2.0.0.dylib /usr/local/lib/gobject-2.0
+sudo ln -s /opt/homebrew/opt/pango/lib/libpango-1.0.dylib /usr/local/lib/pango-1.0
+sudo ln -s /opt/homebrew/opt/harfbuzz/lib/libharfbuzz.dylib /usr/local/lib/harfbuzz
+sudo ln -s /opt/homebrew/opt/fontconfig/lib/libfontconfig.1.dylib /usr/local/lib/fontconfig-1
+sudo ln -s /opt/homebrew/opt/pango/lib/libpangoft2-1.0.dylib /usr/local/lib/pangoft2-1.0
 ```
 
 </details>
 
-Install the dependencies and the package (the `pip install -r requirements_dev.txt` can be skipped on a production server)
+
+#### Install via `conda` [recommended]
+
+If you are using `conda`, we recommend creating a new environment using `conda-lock` to ensure that the environment is reproducible across different systems.
+
+**Create the environment using `conda-lock` [recommended]**
+
+To create a new environment using `conda-lock`, first install `conda-lock`, if you haven't already, using one of the [available methods](https://github.com/conda/conda-lock/tree/main?tab=readme-ov-file#installation). 
+
+Then, run the following command in the root directory of the repository:
 
 ```bash
-pip install -r requirements.txt
-pip install -r requirements_dev.txt
-python setup.py install
+conda-lock install --name <env_name>
 ```
 
-<details>
+This will create a new environment with the name `<env_name>` and install all the required dependencies.
 
-<summary>Note on MacOS installations</summary>
+<details>
 
-### Fix library issues
+<summary>Using default conda [alternative]</summary>
 
-If you are using MacOS, you might run into some issues with the libraries when running the app. 
+#### Create the environment using `conda`
 
-In case you get the `OSError: cannot load library 'gobject-2.0-0'` error (or similar), install `glib` and `pango` via [Homebrew](https://brew.sh/):
+If you prefer to create the environment using `conda` directly, you can use the provided `conda_requirements.yml` file.
 
 ```bash
-brew install glib
-brew install pango
+conda env create -n <env_name> -f conda_requirements.yml
 ```
 
-and then symlink the libraries to `/usr/local/lib`:
+where `<env_name>` is the name of the environment you want to create.  Then, activate the environment with:
 
 ```bash
-sudo ln -s /opt/homebrew/opt/glib/lib/libgobject-2.0.0.dylib /usr/local/lib/gobject-2.0
-sudo ln -s /opt/homebrew/opt/pango/lib/libpango-1.0.dylib /usr/local/lib/pango-1.0
-sudo ln -s /opt/homebrew/opt/harfbuzz/lib/libharfbuzz.dylib /usr/local/lib/harfbuzz
-sudo ln -s /opt/homebrew/opt/fontconfig/lib/libfontconfig.1.dylib /usr/local/lib/fontconfig-1
-sudo ln -s /opt/homebrew/opt/pango/lib/libpangoft2-1.0.dylib /usr/local/lib/pangoft2-1.0
+conda activate <env_name>
 ```
 
 </details>
 
+#### Install via `pip` [alternative]
+
+Install the dependencies and the package (the `pip install -r requirements_dev.txt` can be skipped on a production server)
+
+```bash
+pip install -r requirements.txt
+pip install -r requirements_dev.txt
+python setup.py install
+```
+
 
 ### Configuration