Update doc links (#32)

* fix internal links

* add syntax hints

* Update README.md

fix links

* Add copyright year automatically

Also add version to config

* Create docs-tests.yml

add documentation tests

* Update docs-tests.yml

add linkcheck

* Update annotations.md

break link

* Update annotations.md

Fix broken link

* Update docs-tests.yml

.github/workflows/docs-tests.yml

@@ -0,0 +1,23 @@
+name: "Pull Request Docs Check"
+run-name: "Docs Check 📑📝"
+
+on:
+- pull_request
+
+jobs:
+  docs-build:
+    runs-on: ubuntu-latest
+    steps:
+    - uses: actions/checkout@v3
+    - uses: ammaraskar/sphinx-action@0.4
+      with:
+        docs-folder: "docs/"
+
+  docs-link-check:
+    runs-on: ubuntu-latest
+    steps:
+    - uses: actions/checkout@v3
+    - uses: ammaraskar/sphinx-action@0.4
+      with:
+        docs-folder: "docs/"
+        build-command: "make linkcheck"

README.md

@@ -37,12 +37,12 @@ If you are running on an computing cluster, you will need a [profile](https://gi
 
 ### Run the preprocessing pipeline on VCF files
 
-Instructions [here](https://github.com/PMBio/deeprvat/blob/main/deeprvat/docs/preprocessing.md)
+Instructions [here](https://github.com/PMBio/deeprvat/blob/main/docs/preprocessing.md)
 
 
 ### Annotate variants
 
-Instructions [here](https://github.com/PMBio/deeprvat/blob/main/deeprvat/docs/annotations.md)
+Instructions [here](https://github.com/PMBio/deeprvat/blob/main/docs/annotations.md)
 
 
 

docs/conf.py

@@ -6,10 +6,13 @@
 # -- Project information -----------------------------------------------------
 # https://www.sphinx-doc.org/en/master/usage/configuration.html#project-information
 
+from datetime import datetime
+
 project = "DeepRVAT"
-copyright = "2023, Clarke, B., Holtkamp, E., Öztürk, H., Mück, M., Wahlberg, M., Meyer, K., Brechtmann, F., Hölzlwimmer, F. R., Gagneur, J., & Stegle, O"
+copyright = f"{datetime.now().year}, Clarke, B., Holtkamp, E., Öztürk, H., Mück, M., Wahlberg, M., Meyer, K., Brechtmann, F., Hölzlwimmer, F. R., Gagneur, J., & Stegle, O"
 author = "Clarke, B., Holtkamp, E., Öztürk, H., Mück, M., Wahlberg, M., Meyer, K., Brechtmann, F., Hölzlwimmer, F. R., Gagneur, J., & Stegle, O"
-release = "0.1.0"
+version = "0.1.0"
+release = version
 
 # -- General configuration ---------------------------------------------------
 # https://www.sphinx-doc.org/en/master/usage/configuration.html#general-configuration

docs/usage.md

@@ -3,21 +3,21 @@
 ## Installation
 
 1. Clone this repository:
-```
+```shell
 git clone git@github.com:PMBio/deeprvat.git
 ```
 1. Change directory to the repository: `cd deeprvat`
 1. Install the conda environment. We recommend using [mamba](https://mamba.readthedocs.io/en/latest/index.html), though you may also replace `mamba` with `conda` 
 
    *note: [the current deeprvat env does not support cuda when installed with conda](https://github.com/PMBio/deeprvat/issues/16), install using mamba for cuda support.*
-```
+```shell
 mamba env create -n deeprvat -f deeprvat_env.yaml 
 ```
 1. Activate the environment: `mamba activate deeprvat`
 1. Install the `deeprvat` package: `pip install -e .`
 
 If you don't want to install the gpu related requirements use the `deeprvat_env_no_gpu.yml` environment instead.
-```
+```shell
 mamba env create -n deeprvat -f deeprvat_env_no_gpu.yaml 
 ```
 
@@ -28,23 +28,23 @@ mamba env create -n deeprvat -f deeprvat_env_no_gpu.yaml
 
 Before running any of the snakefiles, you may want to adjust the number of threads used by different steps in the pipeline. To do this, modify the `threads:` property of a given rule.
 
-If you are running on an computing cluster, you will need a [profile](https://github.com/snakemake-profiles) and may need to add `resources:` directives to the snakefiles.
+If you are running on a computing cluster, you will need a [profile](https://github.com/snakemake-profiles) and may need to add `resources:` directives to the snakefiles.
 
 
 ### Run the preprocessing pipeline on VCF files
 
-Instructions [here](https://github.com/PMBio/deeprvat/blob/main/deeprvat/preprocessing/README.md)
+Instructions [here](preprocessing.md)
 
 
 ### Annotate variants
 
-Instructions [here](https://github.com/PMBio/deeprvat/blob/main/deeprvat/annotations/README.md)
+Instructions [here](annotations.md)
 
 
 
 ### Try the full training and association testing pipeline on some example data
 
-```
+```shell
 mkdir example
 cd example
 ln -s [path_to_deeprvat]/example/* .
@@ -58,7 +58,7 @@ Note that the example data is randomly generated, and so is only suited for test
 
 ### Run the association testing pipeline with pretrained models
 
-```
+```shell
 mkdir example
 cd example
 ln -s [path_to_deeprvat]/example/* .