Add instructions to run unit tests locally

README.md

@@ -17,7 +17,7 @@
 
 ## Installation
 
-The recommended way to install `pytximport`is through Bioconda:
+The recommended way to install `pytximport` is through Bioconda:
 
 ```bash
 mamba install -c bioconda pytximpport
@@ -126,6 +126,14 @@ Since `pytximport` is linted and formatted, the repository contains a list of re
 
 For new features and non-obvious bug fixes, we kindly ask that you create a GitHub issue before submitting a PR.
 
+## Running the tests locally
+
+Please follow the steps described in the "Contributing" section. Once you have setup your development environment, you can run the unit tests locally:
+
+```bash
+make coverage-report
+```
+
 ## Building the documentation locally
 
 The documentation can be build locally by navigating to the `docs` folder and running: `make html`.

docs/source/start.md

@@ -17,14 +17,13 @@
 
 ## Installation
 
-The recommended way to install `pytximport`is through Bioconda:
+The recommended way to install `pytximport` is through Bioconda:
 
 ```bash
 mamba install -c bioconda pytximpport
 ```
 
 `pytximport` can also be installed via pip:
-
 ```bash
 pip install pytximport
 ```
@@ -66,8 +65,6 @@ Common options are:
 - `-tx`: Provide this flag to return transcript-level instead of gene-summarized data. Incompatible with gene-level input and `counts_from_abundance=length_scaled_tpm`.
 - `--help`: Display all configuration options.
 
-If you are looking for a full-featured end-to-end workflow for Pythonic bulk RNA-sequencing analysis, check out our [Snakemake workflow](https://github.com/complextissue/snakemake-bulk-rna-seq-workflow/) based on pytximport.
-
 ## Documentation
 
 Detailled documentation is made available at: [https://pytximport.readthedocs.io](https://pytximport.readthedocs.io/en/latest/start.html).
@@ -129,6 +126,14 @@ Since `pytximport` is linted and formatted, the repository contains a list of re
 
 For new features and non-obvious bug fixes, we kindly ask that you create a GitHub issue before submitting a PR.
 
+## Running the tests locally
+
+Please follow the steps described in the "Contributing" section. Once you have setup your development environment, you can run the unit tests locally:
+
+```bash
+make coverage-report
+```
+
 ## Building the documentation locally
 
 The documentation can be build locally by navigating to the `docs` folder and running: `make html`.

pyproject.toml

@@ -102,12 +102,11 @@ log_cli = "true"
 
 markers = [
     "no_github_ci: marks tests that should not be run on GitHub CI (deselect with '-m \"not no_github_ci\"')",
-    "datafiles: takes files provided by pytest-datafiles'",
 ]
 
 [tool.coverage.run]
 source = ["pytximport"]
-omit = ["*/test/*", "*/plot/*"]
+omit = ["*/test/*"]
 
 [tool.coverage.report]
 exclude_lines = [