chore: update installation docs and keep in sync with README (#243)

README.md

@@ -9,18 +9,14 @@ Tooling for connecting GitLab, pipelines, and SODAR at CUBI.
 
 ## Getting Started
 
-Prerequisites when using conda:
+Clone CUBI-TK, create a conda environment and install using [`uv`](https://docs.astral.sh/uv/).
 
 ```bash
+$ git clone [email protected]:bihealth/cubi-tk.git
 $ conda env create -n cubi-tk -f environment.yaml
 $ conda activate cubi-tk
-```
-
-Clone CUBI-TK and install.
-
-```bash
-$ git clone [email protected]:bihealth/cubi-tk.git
 $ cd cubi-tk
+$ uv python pin 3.12
 $ uv sync
 $ uv pip install -e .
 # or, if you need snappy kickoff:
@@ -33,7 +29,7 @@ $ uv pip install -e .
 $ uv sync --all-extras --group docs
 $ cd docs_manual
 $ uv run make clean html
-$ ls _build/html/index.html
+$ xdg-open _build/html/index.html
 ```
 
 ## Argument Completion

docs_manual/installation.rst

@@ -4,38 +4,32 @@
 Installation
 ============
 
-Prerequisites when using conda:
+Clone CUBI-TK, create a conda environment and install using [`uv`](https://docs.astral.sh/uv/).
 
 .. code-block:: bash
 
-  $ conda create -n cubi-tk python=3.10
+  $ git clone [email protected]:bihealth/cubi-tk.git
+  $ conda env create -n cubi-tk -f environment.yaml
   $ conda activate cubi-tk
-
-Clone CUBI-TK and install:
-
-.. code-block:: bash
-
-  $ git clone [email protected]:CUBI/Pipelines/cubi-tk.git
   $ cd cubi-tk
-  $ pip install -e .
-
-For building the manual or running tests you will need some more packages.
-
-.. code-block:: bash
+  $ uv python pin 3.12
+  $ uv sync
+  $ uv pip install -e .
+  # or, if you need snappy kickoff:
+  #$ GIT_LFS_SKIP_SMUDGE=1 uv pip install -e '.[snappy]'
 
-  $ pip install -r requirements/develop.txt
 
 Run tests
 ---------
 
 .. code-block:: bash
 
-  $ make test
+  $ uv run make pytest
 
 Build manual
 ------------
 
 .. code-block:: bash
 
   $ cd docs_manual
-  $ make clean html
+  $ uv run make clean html

environment.yaml

@@ -6,10 +6,11 @@ channels:
 name: cubi-tk
 
 dependencies:
-  - python >=3.9
+  - python ~=3.12
   - pip
   - uv >=0.5
   - pysam >=0.22
   - vcfpy >=0.13.8
   - gcc_linux-64 >=13,<14
   - zlib ~=1.3.0
+  - liblzma ~=5.6.3