alphadia 1.9.3.dev2__tar.gz → 1.12.2__tar.gz

{alphadia-1.9.3.dev2/alphadia.egg-info → alphadia-1.12.2}/PKG-INFO

@@ -1,6 +1,6 @@
-Metadata-Version: 2.2
+Metadata-Version: 2.4
 Name: alphadia
-Version: 1.9.3.dev2
+Version: 1.12.2
 Summary: A novel proteomics search engine for DIA data based on end-to-end transfer learning.
 Author-email: Mann Labs <wallmann@biochem.mpg.de>
 License:                                  Apache License
@@ -205,11 +205,14 @@ License:                                  Apache License
            See the License for the specific language governing permissions and
            limitations under the License.
         
-Project-URL: Paper preprint, https://www.biochem.mpg.de/mann
-Project-URL: Repository, https://github.com/MannLabs/alphadia
-Project-URL: Issues, https://github.com/MannLabs/alphadia/issues
+Project-URL: repository, https://github.com/MannLabs/alphadia
+Project-URL: issues, https://github.com/MannLabs/alphadia/issues
+Project-URL: download, https://github.com/MannLabs/alphadia/releases
+Project-URL: homepage, https://www.alphapept.org
 Project-URL: Mann Labs Homepage, https://www.biochem.mpg.de/mann
-Keywords: mass spectrometry,proteomics,search engine,DIA,data-independent acquisition,bioinformatics,AlphaPept,AlphaPept ecosystem
+Project-URL: publication, https://doi.org/10.1038/s41587-025-02791-w
+Project-URL: documentation, https://alphadia.readthedocs.io/en/latest/
+Keywords: mass spectrometry,proteomics,search engine,DIA,data-independent acquisition,bioinformatics,AlphaPept,AlphaPept ecosystem,alphapept.org
 Classifier: Development Status :: 4 - Beta
 Classifier: Intended Audience :: Science/Research
 Classifier: License :: OSI Approved :: Apache Software License
@@ -219,51 +222,112 @@ Classifier: Topic :: Scientific/Engineering :: Bio-Informatics
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@@ -273,21 +337,23 @@ Requires-Dist: pandoc; extra == "docs"
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+Dynamic: license-file
 
 ![GitHub Release](https://img.shields.io/github/v/release/mannlabs/alphadia?logoColor=green&color=brightgreen)
 ![Versions](https://img.shields.io/badge/python-3.10_%7C_3.11_%7C_3.12-brightgreen)
@@ -316,6 +382,8 @@ Requires-Dist: pandoc; extra == "development"
     <a href="https://github.com/MannLabs/alphadia/discussions">Discussion</a>
     ·
     <a href="https://alphadia.readthedocs.io/en/latest/">Documentation</a>
+    ·
+    <a href="https://alphapept.org">alphapept.org</a>
   </p>
 </div>
 
@@ -336,19 +404,16 @@ We support the following vendor and processing modes:
 | Bruker .d |  ✅   | ⚠️ |
 > ⚠️ **Predicted libraries with Bruker .d data**<br>Alltough search is possible, alphaDIA's feature-free search takes a long time with fully predicted libraries. We are still evaluating how to better support fully predicted libraries.
 
-## Manuscript
-**Please cite:**
-> **AlphaDIA enables End-to-End Transfer Learning for Feature-Free Proteomics**<br>
-> Georg Wallmann, Patricia Skowronek, Vincenth Brennsteiner, Mikhail Lebedev, Marvin Thielert, Sophia Steigerwald, Mohamed Kotb, Tim Heymann, Xie-Xuan Zhou, Magnus Schwörer, Maximilian T. Strauss, Constantin Ammar, Sander Willems, Wen-Feng Zeng, Matthias Mann<br>
-> [biorxiv.org](https://www.biorxiv.org/content/10.1101/2024.05.28.596182v1)
 
-alphaDIA is part of the alphaX ecosystem:
-- [alphaPept](https://github.com/MannLabs/alphapept)
+
+alphaDIA is part of the [alphapept ecosystem](https://alphapept.org):
+- [alphaBase](https://github.com/MannLabs/alphabase)
+- [alphaRaw](https://github.com/MannLabs/alpharaw)
 - [alphaTims](https://github.com/MannLabs/alphatims)
+- [alphaPept](https://github.com/MannLabs/alphapept)
 - [alphaPeptDeep](https://github.com/MannLabs/alphapeptdeep)
-- [alphaRaw](https://github.com/MannLabs/alpharaw)
-- [alphaBase](https://github.com/MannLabs/alphabase)
 - [directLFQ](https://github.com/MannLabs/directlfq)
+- [alphaQuant](https://github.com/MannLabs/alphaquant)
 
 ## Installation
 
@@ -365,15 +430,34 @@ AlphaDIA can be installed on Windows, macOS and Linux. Please choose the preferr
 * [**Slurm installation:**](docs/installation.md#slurm-cluster-installation) Choose this for running alphaDIA on a research cluster with Slurm.
 
 ### One-click GUI installation
-Currently available for **MacOS** and **Windows**.
 You can download the latest release of alphaDIA [here](https://github.com/Mannlabs/alphadia/releases/latest).
 
-* **Windows:** Download the latest `alphadia-X.Y.Z-windows-amd64.exe` build and double click it to install. If you receive a warning during installation click *Run anyway*.
-* **MacOS:** Download the latest build suitable for your chip architecture
+
+#### Windows
+Download the latest `alphadia-X.Y.Z-windows-amd64.exe` build and double click it to install. If you receive a warning during installation click *Run anyway*.
+Important note: always install AlphaDIA into a new folder, as the installer will not properly overwrite existing installations.
+
+#### Linux
+If you want to search `.raw` files from Thermo instruments or `.wiff` files from Sciex instruments, [AlphaRaw](https://github.com/MannLabs/alpharaw) is required, which depends on Mono.
+A detailed guide to installing AlphaRaw with mono can be found [here](https://github.com/MannLabs/alpharaw#installation).
+
+Download the latest `alphadia-X.Y.Z-linux-x64.deb` build and install it via `dpkg -i alphadia-X.Y.Z-linux-x64.deb`.
+
+#### MacOS
+If you want to search `.raw` files from Thermo instruments or `.wiff` files from Sciex instruments, [AlphaRaw](https://github.com/MannLabs/alpharaw) is required, which depends on Mono.
+A detailed guide to installing AlphaRaw with mono can be found [here](https://github.com/MannLabs/alpharaw#installation).
+
+Download the latest build suitable for your chip architecture
 (can be looked up by clicking on the Apple Symbol > *About this Mac* > *Chip* ("M1", "M2", "M3" -> `arm64`, "Intel" -> `x64`),
 `alphadia-X.Y.Z-macos-darwin-arm64.pkg` or `alphadia-X.Y.Z-macos-darwin-x64.pkg`. Open the parent folder of the downloaded file in Finder,
-right-click and select *open*. If you receive a warning during installation click *Open*. If you want to use `.raw` files on Thermo instruments alphaRaw is required, which depends on Mono. A detailed guide to installing alphaRaw with mono can be found [here](https://github.com/MannLabs/alpharaw#installation).
-* **Linux:** Download the latest `alphadia-X.Y.Z-linux-x64.deb` build and install it via `dpkg -i alphadia-X.Y.Z-linux-x64.deb`.
+right-click and select *open*. If you receive a warning during installation click *Open*.
+
+In newer MacOS versions, additional steps are required to enable installation of unverified software.
+This is indicated by a dialog telling you `“alphadia. ... .pkg” Not Opened`.
+1. Close this dialog by clicking `Done`.
+2. Choose `Apple menu` > `System Settings`, then `Privacy & Security` in the sidebar. (You may need to scroll down.)
+3. Go to `Security`, locate the line "alphadia.pkg was blocked to protect your Mac" then click `Open Anyway`.
+4. In the dialog windows, click `Open Anyway`.
 
 
 As of now, **Linux** users need follow the steps for the
@@ -387,10 +471,10 @@ you can install alphaDIA via `pip`.
 Please make sure you have a valid installation of conda or miniconda.
 We recommend setting up miniconda as described on their [website](https://docs.conda.io/projects/miniconda/en/latest/).
 
-If you want to use `.raw` files on Thermo instruments alphaRaw is required, which depends on Mono. A detailed guide to installing alphaRaw with mono can be found [here](https://github.com/MannLabs/alpharaw#installation).
+If you want to use `.raw` files on Thermo instruments alphaRaw is required, which depends on Mono. A detailed guide to installing AlphaRaw with mono can be found [here](https://github.com/MannLabs/alpharaw#installation).
 
 #### 2. Setting up the environment
-For any Python package, it is highly recommended to use a separate, as otherwise dependancy conflicts can occur with already existing packages. We generally recommend [miniconda](https://docs.anaconda.com/free/miniconda/).
+For any Python package, it is highly recommended to use a separate, as otherwise dependency conflicts can occur with already existing packages. We generally recommend [miniconda](https://docs.anaconda.com/free/miniconda/).
 
 Finally, alphaDIA and all its dependencies can be installed by
 ```bash
@@ -404,7 +488,7 @@ Alternatively, use
 version clashes if alphaDIA is imported as a library into a defined python requirement.
 Note however, that this "loose" version might be affected e.g. by breaking changes of third-party dependencies.
 
-Finally, run `alphadia -v` to check if the installation was successful;
+Finally, run `alphadia --check` to check if the installation was successful;
 `alphadia -h` will give you a list of command-line options.
 
 ---
@@ -449,13 +533,25 @@ In case of issues, check out the following:
 * [Issues](https://github.com/MannLabs/alphadia/issues): Try a few different search terms to find out if a similar problem has been encountered before
 * [Discussions](https://github.com/MannLabs/alphadia/discussions): Check if your problem or feature requests has been discussed before.
 
+### Problem: Error when downloading the peptdeep pretrained models
+If on startup you receive an error like
+`FileNotFoundError: [Errno 2] No such file or directory: '<some_directory>/peptdeep/pretrained_models'`,
+it could be due to missing write permissions on `<some_directory>`.
+
+#### Solution
+For now, you need to create this directory yourself and manually download the file
+```
+mkdir -p <some_directory>/peptdeep/pretrained_models && cd <some_directory>/peptdeep/pretrained_models
+wget https://github.com/MannLabs/alphapeptdeep/releases/download/pre-trained-models/pretrained_models.zip
+```
+
 ---
 ## Citations
 
-A manuscript has been submitted to bioRxiv:
-> **AlphaDIA enables End-to-End Transfer Learning for Feature-Free Proteomics**
-> Georg Wallmann, Patricia Skowronek, Vincenth Brennsteiner, Mikhail Lebedev, Marvin Thielert, Sophia Steigerwald, Mohamed Kotb, Tim Heymann, Xie-Xuan Zhou, Magnus Schwörer, Maximilian T. Strauss, Constantin Ammar, Sander Willems, Wen-Feng Zeng, Matthias Mann
-> bioRxiv 2024.05.28.596182; doi: https://doi.org/10.1101/2024.05.28.596182
+**Please cite:**
+> **AlphaDIA enables DIA transfer learning for feature-free proteomics**<br>
+> Georg Wallmann, Patricia Skowronek, Vincenth Brennsteiner, Mikhail Lebedev, Marvin Thielert, Sophia Steigerwald, Mohamed Kotb, Oscar Despard, Tim Heymann, Xie-Xuan Zhou, Maximilian T. Strauss, Constantin Ammar, Sander Willems, Magnus Schwörer, Wen-Feng Zeng & Matthias Mann
+> [Nature Biotechnology (2025)](https://doi.org/10.1038/s41587-025-02791-w)
 
 ---
 ## How to contribute
@@ -467,16 +563,16 @@ Further information on the development process can be found [here](docs/installa
 ---
 ## Changelog
 
-See the [HISTORY.md](HISTORY.md) for a full overview of the changes made in each version.
+See the [GitHub releases](https://github.com/MannLabs/alphadia/releases) for a full overview of the changes made in each version.
 
 ---
 ## About
 
-An open-source Python package of the AlphaPept ecosystem from the [Mann Labs at the Max Planck Institute of Biochemistry](https://www.biochem.mpg.de/mann).
+An open-source Python package of the [AlphaPept ecosystem](https://alphapept.org) from the [Mann Labs at the Max Planck Institute of Biochemistry](https://www.biochem.mpg.de/mann).
 
 ---
 ## License
 
-AlphaDIA was developed by the [Mann Labs at the Max Planck Institute of Biochemistry](https://www.biochem.mpg.de/mann) and is freely available with an [Apache License](LICENSE.txt). External Python packages (available in the [requirements](requirements) folder) have their own licenses, which can be consulted on their respective websites.
+AlphaDIA is developed by the [Mann Labs at the Max Planck Institute of Biochemistry](https://www.biochem.mpg.de/mann) and is freely available with an [Apache License](LICENSE.txt). External Python packages (available in the [requirements](requirements) folder) have their own licenses, which can be consulted on their respective websites.
 
 ---

{alphadia-1.9.3.dev2 → alphadia-1.12.2}/README.md

@@ -25,6 +25,8 @@
     <a href="https://github.com/MannLabs/alphadia/discussions">Discussion</a>
     ·
     <a href="https://alphadia.readthedocs.io/en/latest/">Documentation</a>
+    ·
+    <a href="https://alphapept.org">alphapept.org</a>
   </p>
 </div>
 
@@ -45,19 +47,16 @@ We support the following vendor and processing modes:
 | Bruker .d |  ✅   | ⚠️ |
 > ⚠️ **Predicted libraries with Bruker .d data**<br>Alltough search is possible, alphaDIA's feature-free search takes a long time with fully predicted libraries. We are still evaluating how to better support fully predicted libraries.
 
-## Manuscript
-**Please cite:**
-> **AlphaDIA enables End-to-End Transfer Learning for Feature-Free Proteomics**<br>
-> Georg Wallmann, Patricia Skowronek, Vincenth Brennsteiner, Mikhail Lebedev, Marvin Thielert, Sophia Steigerwald, Mohamed Kotb, Tim Heymann, Xie-Xuan Zhou, Magnus Schwörer, Maximilian T. Strauss, Constantin Ammar, Sander Willems, Wen-Feng Zeng, Matthias Mann<br>
-> [biorxiv.org](https://www.biorxiv.org/content/10.1101/2024.05.28.596182v1)
 
-alphaDIA is part of the alphaX ecosystem:
-- [alphaPept](https://github.com/MannLabs/alphapept)
+
+alphaDIA is part of the [alphapept ecosystem](https://alphapept.org):
+- [alphaBase](https://github.com/MannLabs/alphabase)
+- [alphaRaw](https://github.com/MannLabs/alpharaw)
 - [alphaTims](https://github.com/MannLabs/alphatims)
+- [alphaPept](https://github.com/MannLabs/alphapept)
 - [alphaPeptDeep](https://github.com/MannLabs/alphapeptdeep)
-- [alphaRaw](https://github.com/MannLabs/alpharaw)
-- [alphaBase](https://github.com/MannLabs/alphabase)
 - [directLFQ](https://github.com/MannLabs/directlfq)
+- [alphaQuant](https://github.com/MannLabs/alphaquant)
 
 ## Installation
 
@@ -74,15 +73,34 @@ AlphaDIA can be installed on Windows, macOS and Linux. Please choose the preferr
 * [**Slurm installation:**](docs/installation.md#slurm-cluster-installation) Choose this for running alphaDIA on a research cluster with Slurm.
 
 ### One-click GUI installation
-Currently available for **MacOS** and **Windows**.
 You can download the latest release of alphaDIA [here](https://github.com/Mannlabs/alphadia/releases/latest).
 
-* **Windows:** Download the latest `alphadia-X.Y.Z-windows-amd64.exe` build and double click it to install. If you receive a warning during installation click *Run anyway*.
-* **MacOS:** Download the latest build suitable for your chip architecture
+
+#### Windows
+Download the latest `alphadia-X.Y.Z-windows-amd64.exe` build and double click it to install. If you receive a warning during installation click *Run anyway*.
+Important note: always install AlphaDIA into a new folder, as the installer will not properly overwrite existing installations.
+
+#### Linux
+If you want to search `.raw` files from Thermo instruments or `.wiff` files from Sciex instruments, [AlphaRaw](https://github.com/MannLabs/alpharaw) is required, which depends on Mono.
+A detailed guide to installing AlphaRaw with mono can be found [here](https://github.com/MannLabs/alpharaw#installation).
+
+Download the latest `alphadia-X.Y.Z-linux-x64.deb` build and install it via `dpkg -i alphadia-X.Y.Z-linux-x64.deb`.
+
+#### MacOS
+If you want to search `.raw` files from Thermo instruments or `.wiff` files from Sciex instruments, [AlphaRaw](https://github.com/MannLabs/alpharaw) is required, which depends on Mono.
+A detailed guide to installing AlphaRaw with mono can be found [here](https://github.com/MannLabs/alpharaw#installation).
+
+Download the latest build suitable for your chip architecture
 (can be looked up by clicking on the Apple Symbol > *About this Mac* > *Chip* ("M1", "M2", "M3" -> `arm64`, "Intel" -> `x64`),
 `alphadia-X.Y.Z-macos-darwin-arm64.pkg` or `alphadia-X.Y.Z-macos-darwin-x64.pkg`. Open the parent folder of the downloaded file in Finder,
-right-click and select *open*. If you receive a warning during installation click *Open*. If you want to use `.raw` files on Thermo instruments alphaRaw is required, which depends on Mono. A detailed guide to installing alphaRaw with mono can be found [here](https://github.com/MannLabs/alpharaw#installation).
-* **Linux:** Download the latest `alphadia-X.Y.Z-linux-x64.deb` build and install it via `dpkg -i alphadia-X.Y.Z-linux-x64.deb`.
+right-click and select *open*. If you receive a warning during installation click *Open*.
+
+In newer MacOS versions, additional steps are required to enable installation of unverified software.
+This is indicated by a dialog telling you `“alphadia. ... .pkg” Not Opened`.
+1. Close this dialog by clicking `Done`.
+2. Choose `Apple menu` > `System Settings`, then `Privacy & Security` in the sidebar. (You may need to scroll down.)
+3. Go to `Security`, locate the line "alphadia.pkg was blocked to protect your Mac" then click `Open Anyway`.
+4. In the dialog windows, click `Open Anyway`.
 
 
 As of now, **Linux** users need follow the steps for the
@@ -96,10 +114,10 @@ you can install alphaDIA via `pip`.
 Please make sure you have a valid installation of conda or miniconda.
 We recommend setting up miniconda as described on their [website](https://docs.conda.io/projects/miniconda/en/latest/).
 
-If you want to use `.raw` files on Thermo instruments alphaRaw is required, which depends on Mono. A detailed guide to installing alphaRaw with mono can be found [here](https://github.com/MannLabs/alpharaw#installation).
+If you want to use `.raw` files on Thermo instruments alphaRaw is required, which depends on Mono. A detailed guide to installing AlphaRaw with mono can be found [here](https://github.com/MannLabs/alpharaw#installation).
 
 #### 2. Setting up the environment
-For any Python package, it is highly recommended to use a separate, as otherwise dependancy conflicts can occur with already existing packages. We generally recommend [miniconda](https://docs.anaconda.com/free/miniconda/).
+For any Python package, it is highly recommended to use a separate, as otherwise dependency conflicts can occur with already existing packages. We generally recommend [miniconda](https://docs.anaconda.com/free/miniconda/).
 
 Finally, alphaDIA and all its dependencies can be installed by
 ```bash
@@ -113,7 +131,7 @@ Alternatively, use
 version clashes if alphaDIA is imported as a library into a defined python requirement.
 Note however, that this "loose" version might be affected e.g. by breaking changes of third-party dependencies.
 
-Finally, run `alphadia -v` to check if the installation was successful;
+Finally, run `alphadia --check` to check if the installation was successful;
 `alphadia -h` will give you a list of command-line options.
 
 ---
@@ -158,13 +176,25 @@ In case of issues, check out the following:
 * [Issues](https://github.com/MannLabs/alphadia/issues): Try a few different search terms to find out if a similar problem has been encountered before
 * [Discussions](https://github.com/MannLabs/alphadia/discussions): Check if your problem or feature requests has been discussed before.
 
+### Problem: Error when downloading the peptdeep pretrained models
+If on startup you receive an error like
+`FileNotFoundError: [Errno 2] No such file or directory: '<some_directory>/peptdeep/pretrained_models'`,
+it could be due to missing write permissions on `<some_directory>`.
+
+#### Solution
+For now, you need to create this directory yourself and manually download the file
+```
+mkdir -p <some_directory>/peptdeep/pretrained_models && cd <some_directory>/peptdeep/pretrained_models
+wget https://github.com/MannLabs/alphapeptdeep/releases/download/pre-trained-models/pretrained_models.zip
+```
+
 ---
 ## Citations
 
-A manuscript has been submitted to bioRxiv:
-> **AlphaDIA enables End-to-End Transfer Learning for Feature-Free Proteomics**
-> Georg Wallmann, Patricia Skowronek, Vincenth Brennsteiner, Mikhail Lebedev, Marvin Thielert, Sophia Steigerwald, Mohamed Kotb, Tim Heymann, Xie-Xuan Zhou, Magnus Schwörer, Maximilian T. Strauss, Constantin Ammar, Sander Willems, Wen-Feng Zeng, Matthias Mann
-> bioRxiv 2024.05.28.596182; doi: https://doi.org/10.1101/2024.05.28.596182
+**Please cite:**
+> **AlphaDIA enables DIA transfer learning for feature-free proteomics**<br>
+> Georg Wallmann, Patricia Skowronek, Vincenth Brennsteiner, Mikhail Lebedev, Marvin Thielert, Sophia Steigerwald, Mohamed Kotb, Oscar Despard, Tim Heymann, Xie-Xuan Zhou, Maximilian T. Strauss, Constantin Ammar, Sander Willems, Magnus Schwörer, Wen-Feng Zeng & Matthias Mann
+> [Nature Biotechnology (2025)](https://doi.org/10.1038/s41587-025-02791-w)
 
 ---
 ## How to contribute
@@ -176,16 +206,16 @@ Further information on the development process can be found [here](docs/installa
 ---
 ## Changelog
 
-See the [HISTORY.md](HISTORY.md) for a full overview of the changes made in each version.
+See the [GitHub releases](https://github.com/MannLabs/alphadia/releases) for a full overview of the changes made in each version.
 
 ---
 ## About
 
-An open-source Python package of the AlphaPept ecosystem from the [Mann Labs at the Max Planck Institute of Biochemistry](https://www.biochem.mpg.de/mann).
+An open-source Python package of the [AlphaPept ecosystem](https://alphapept.org) from the [Mann Labs at the Max Planck Institute of Biochemistry](https://www.biochem.mpg.de/mann).
 
 ---
 ## License
 
-AlphaDIA was developed by the [Mann Labs at the Max Planck Institute of Biochemistry](https://www.biochem.mpg.de/mann) and is freely available with an [Apache License](LICENSE.txt). External Python packages (available in the [requirements](requirements) folder) have their own licenses, which can be consulted on their respective websites.
+AlphaDIA is developed by the [Mann Labs at the Max Planck Institute of Biochemistry](https://www.biochem.mpg.de/mann) and is freely available with an [Apache License](LICENSE.txt). External Python packages (available in the [requirements](requirements) folder) have their own licenses, which can be consulted on their respective websites.
 
 ---

alphadia-1.12.2/alphadia/__init__.py

@@ -0,0 +1,9 @@
+#!python
+
+import warnings
+
+__version__ = "1.12.2"
+
+warnings.filterwarnings(
+    "ignore", message="Dependency 'dask' not installed.", module="directlfq"
+)