alphapepttools 0.3.0__tar.gz → 0.4.1.dev0__tar.gz

{alphapepttools-0.3.0 → alphapepttools-0.4.1.dev0}/.bumpversion.toml

@@ -1,5 +1,5 @@
 [tool.bumpversion]
-current_version = "0.3.0"
+current_version = "0.4.1-dev0"
 parse = """(?x)
     (?P<major>0|[1-9]\\d*)\\.
     (?P<minor>0|[1-9]\\d*)\\.

{alphapepttools-0.3.0 → alphapepttools-0.4.1.dev0}/.github/workflows/test.yaml

@@ -91,4 +91,4 @@ jobs:
         run: |
           coverage report
       - name: Upload coverage
-        uses: codecov/codecov-action@v7.0.0
+        uses: codecov/codecov-action@v7.1.1

{alphapepttools-0.3.0 → alphapepttools-0.4.1.dev0}/PKG-INFO

@@ -1,6 +1,6 @@
 Metadata-Version: 2.5
 Name: alphapepttools
-Version: 0.3.0
+Version: 0.4.1-dev0
 Summary: Search- and quantification-engine agnostic biological interpretation of proteomics data
 Project-URL: Documentation, https://alphapepttools.readthedocs.io/
 Project-URL: Homepage, https://github.com/MannLabs/alphapepttools
@@ -227,6 +227,7 @@ Requires-Dist: pyarrow
 Requires-Dist: scanpy
 Requires-Dist: scikit-learn
 Requires-Dist: session-info2
+Requires-Dist: tqdm
 Provides-Extra: dev
 Requires-Dist: pre-commit; extra == 'dev'
 Requires-Dist: twine>=4.0.2; extra == 'dev'
@@ -263,6 +264,7 @@ Requires-Dist: pyarrow==23.0.1; extra == 'stable'
 Requires-Dist: scanpy==1.11.5; extra == 'stable'
 Requires-Dist: scikit-learn==1.8; extra == 'stable'
 Requires-Dist: session-info2==0.4; extra == 'stable'
+Requires-Dist: tqdm==4.70; extra == 'stable'
 Provides-Extra: test
 Requires-Dist: coverage; extra == 'test'
 Requires-Dist: nbmake; extra == 'test'
@@ -274,12 +276,17 @@ Description-Content-Type: text/markdown
 ![PyPI - Version](https://img.shields.io/pypi/v/alphapepttools)
 [![Tests][badge-tests]][tests]
 [![Documentation][badge-docs]][documentation]
+[![Preprint][badge-preprint]][preprint]
 
 [badge-tests]: https://img.shields.io/github/actions/workflow/status/MannLabs/alphapepttools/test.yaml?branch=main
 [badge-docs]: https://github.com/MannLabs/alphapepttools/actions/workflows/docs.yaml/badge.svg
+[badge-preprint]: https://img.shields.io/badge/preprint-bioRxiv-b31b1b
 
 Search- and quantification-engine agnostic downstream processing of proteomics data
 
+> [!TIP]
+> Our [preprint is out now][preprint]!
+
 ## `alphapepttools` was made to make your life in proteomics easier!
 
 Functionalities are intended to be as close to pure python as possible, avoiding closed end-to-end implementations, which is reflected in several design choices:
@@ -305,7 +312,7 @@ in particular, the [API documentation][].
 
 ## Installation
 
-You need to have Python 3.11 or newer installed on your system.
+You need to have Python 3.11 or newer installed on your system (Linux/MacOS/Windows).
 If you don't have Python installed, we recommend installing [Mambaforge][].
 
 There are several alternative options to install alphapepttools:
@@ -324,6 +331,9 @@ As the package is still under development, consider installing the latest develo
 pip install git+https://github.com/MannLabs/alphapepttools.git@main
 ```
 
+For a full list of dependencies, see the dependencies section in the [pyproject.toml](pyproject.toml).
+Installation should take less than 5 minutes.
+
 ### Installation extras
 
 Depending on your use case, you might want to install specific versions of packages or additional dependencies.
@@ -380,12 +390,14 @@ If you found a bug, please use the [issue tracker][].
 
 ## Citation
 
-> t.b.a
+> Brennsteiner, V., Diedrich, L. et al.
+> [_AlphaPeptTools: scverse-native analysis of mass spectrometry-based proteomics_][preprint] (preprint), bioRxiv (2026).
 
 [mambaforge]: https://github.com/conda-forge/miniforge#mambaforge
 [scverse discourse]: https://discourse.scverse.org/
 [issue tracker]: https://github.com/MannLabs/alphapepttools/issues
 [tests]: https://github.com/MannLabs/alphapepttools/actions/workflows/test.yml
+[preprint]: https://www.biorxiv.org/content/10.64898/2026.09.11.750886v1
 
 <!-- TODO: Change documentation pages back to readthedocs upon public release -->
 <!-- [documentation]: https://alphapepttools.readthedocs.io -->

{alphapepttools-0.3.0 → alphapepttools-0.4.1.dev0}/README.md

@@ -3,12 +3,17 @@
 ![PyPI - Version](https://img.shields.io/pypi/v/alphapepttools)
 [![Tests][badge-tests]][tests]
 [![Documentation][badge-docs]][documentation]
+[![Preprint][badge-preprint]][preprint]
 
 [badge-tests]: https://img.shields.io/github/actions/workflow/status/MannLabs/alphapepttools/test.yaml?branch=main
 [badge-docs]: https://github.com/MannLabs/alphapepttools/actions/workflows/docs.yaml/badge.svg
+[badge-preprint]: https://img.shields.io/badge/preprint-bioRxiv-b31b1b
 
 Search- and quantification-engine agnostic downstream processing of proteomics data
 
+> [!TIP]
+> Our [preprint is out now][preprint]!
+
 ## `alphapepttools` was made to make your life in proteomics easier!
 
 Functionalities are intended to be as close to pure python as possible, avoiding closed end-to-end implementations, which is reflected in several design choices:
@@ -34,7 +39,7 @@ in particular, the [API documentation][].
 
 ## Installation
 
-You need to have Python 3.11 or newer installed on your system.
+You need to have Python 3.11 or newer installed on your system (Linux/MacOS/Windows).
 If you don't have Python installed, we recommend installing [Mambaforge][].
 
 There are several alternative options to install alphapepttools:
@@ -53,6 +58,9 @@ As the package is still under development, consider installing the latest develo
 pip install git+https://github.com/MannLabs/alphapepttools.git@main
 ```
 
+For a full list of dependencies, see the dependencies section in the [pyproject.toml](pyproject.toml).
+Installation should take less than 5 minutes.
+
 ### Installation extras
 
 Depending on your use case, you might want to install specific versions of packages or additional dependencies.
@@ -109,12 +117,14 @@ If you found a bug, please use the [issue tracker][].
 
 ## Citation
 
-> t.b.a
+> Brennsteiner, V., Diedrich, L. et al.
+> [_AlphaPeptTools: scverse-native analysis of mass spectrometry-based proteomics_][preprint] (preprint), bioRxiv (2026).
 
 [mambaforge]: https://github.com/conda-forge/miniforge#mambaforge
 [scverse discourse]: https://discourse.scverse.org/
 [issue tracker]: https://github.com/MannLabs/alphapepttools/issues
 [tests]: https://github.com/MannLabs/alphapepttools/actions/workflows/test.yml
+[preprint]: https://www.biorxiv.org/content/10.64898/2026.09.11.750886v1
 
 <!-- TODO: Change documentation pages back to readthedocs upon public release -->
 <!-- [documentation]: https://alphapepttools.readthedocs.io -->

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