Limit git clone to one commit, more extensive documentation, contribu…

…ting information

.gitignore

@@ -43,6 +43,9 @@ ENV/
 .dmypy.json
 dmypy.json
 
+# Ruff
+.ruff_cache/
+
 # Pyre type checker
 .pyre/
 

README.md

@@ -107,6 +107,25 @@ Features unique to `tximport`
 
 Argument order and argument defaults may differ between the implementations.
 
+## Contributing
+
+Contributions are welcome. Contributors are asked to follow the Contributor Covenant Code of Conduct.
+
+To set up `pytximport` for development on your machine, we recommend to git clone the dev branch:
+
+```bash
+git clone --depth 1 -b dev https://github.com/complextissue/pytximport.git
+cd pytximport
+pyenv local 3.9
+make create-venv
+source .venv/source/activate
+make install-dev
+```
+
+Since `pytximport` is linted and formatted, the repository contains a list of recommended VS Code extensions in `.vscode/extensions.json`. If you are using a different editor, please make sure to set up your environment to use the same linters and formatters.
+
+For new features and non-obvious bug fixes, we kindly ask that you create a GitHub issue before submitting a PR.
+
 ## Building the documentation locally
 
 The documentation can be build locally by navigating to the `docs` folder and running: `make html`.

docs/source/installation.md

@@ -49,7 +49,7 @@ This option is only recommended for potential contributors and installs addition
 Install `pytximport` from source:
 
 ```bash
-git clone https://github.com/complextissue/pytximport.git
+git clone --depth 1 -b dev https://github.com/complextissue/pytximport.git
 cd pytximport
 pyenv local 3.9
 make create-venv

docs/source/start.md

@@ -24,6 +24,7 @@ mamba install -c bioconda pytximpport
 ```
 
 `pytximport` can also be installed via pip:
+
 ```bash
 pip install pytximport
 ```
@@ -65,6 +66,8 @@ 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).
@@ -107,6 +110,25 @@ Features unique to `tximport`
 
 Argument order and argument defaults may differ between the implementations.
 
+## Contributing
+
+Contributions are welcome. Contributors are asked to follow the Contributor Covenant Code of Conduct.
+
+To set up `pytximport` for development on your machine, we recommend to git clone the dev branch:
+
+```bash
+git clone --depth 1 -b dev https://github.com/complextissue/pytximport.git
+cd pytximport
+pyenv local 3.9
+make create-venv
+source .venv/source/activate
+make install-dev
+```
+
+Since `pytximport` is linted and formatted, the repository contains a list of recommended VS Code extensions in `.vscode/extensions.json`. If you are using a different editor, please make sure to set up your environment to use the same linters and formatters.
+
+For new features and non-obvious bug fixes, we kindly ask that you create a GitHub issue before submitting a PR.
+
 ## Building the documentation locally
 
 The documentation can be build locally by navigating to the `docs` folder and running: `make html`.

pytximport/__init__.py

@@ -1,16 +1,26 @@
-"""pytximport: Convert transcript-level expression to gene-level expression.
+"""pytximport: Gene-level count estimation from transcript quantification files
 
-The `pytximport` package provides a Python implementation of the `tximport` R package, which converts transcript-level
-expression to gene-level count estimates.
+The `pytximport` package provides a Python implementation of the `tximport` R package, which provides an easy-to-use
+interface for importing transcript quantification files from various tools (e.g., `salmon`, `kallisto`, `RSEM`) into
+Python. The package is designed to work with the output of these tools and provide isoform bias-corrected gene-level
+counts for downstream analysis.
+
+The package provides a single function, `tximport`, as the main entry point, as well as a command-line interface
+(`pytximport`). Further utility functions (e.g., to create a transcript-to-gene map) are provided through the
+`pytximport.utils` module.
+
+`pytximport` can output data as AnnData objects and xarray objects or save the data as a CSV file, enabling seamless
+integration with other Python packages such as `PyDESeq2`.
 
 .. note::
-    Please also cite the original `tximport` R package when using `pytximport`.
-    DOI: https://doi.org/10.12688/f1000research.7563.1
+    Please consider citing both `pytximport` and the original R implementation of `tximport` when using `pytximport`.
+    For `pytximport`, please refer to the README or CITATION.cff file for the appropriate citation information.
+    The original `tximport` publication can be found at: https://doi.org/10.12688/f1000research.7563.1
 
 .. warning::
-    The `pytximport` package is still in development and currently does not support alevin quantification files,
-    unlike the `tximport` R package. Default parameters, argument names and return types may also differ between the
-    implementations.
+    Though `pytximport` aims to provide the same functionality as `tximport`, there are some differences between the two
+    packages. While the same configuration will result in identical output, the configuration options and defaults may
+    differ between the two packages. Please refer to the documentation for more information.
 """
 
 from . import definitions, importers, utils
@@ -20,6 +30,3 @@
 
 # Allow users to import the tximport function as pytximport as well
 pytximport = tximport
-
-create_transcript_gene_map = utils.create_transcript_gene_map
-create_transcript_gene_map_from_annotation = utils.create_transcript_gene_map_from_annotation