Improve docs and functionality

.github/workflows/publish.yml

@@ -1,39 +1,39 @@
-name: Publish
-
-on:
-  workflow_dispatch:
-  release:
-    types: [created]
-
-jobs:
-  publish:
-    runs-on: ubuntu-latest
-    environment:
-      name: pypi
-      url: https://pypi.org/p/im2deep
-    permissions:
-      id-token: write
-    steps:
-      - uses: actions/checkout@v4
-
-      - name: Set up Python
-        uses: actions/setup-python@v4
-        with:
-          python-version: "3.8"
-
-      - name: Install dependencies
-        run: |
-          python -m pip install --upgrade pip build
-
-      - name: Build
-        run: python -m build
-
-      - name: Install
-        run: pip install dist/im2deep-*.whl
-
-      - name: Test package
-        run: |
-          im2deep --help
-
-      - name: Publish to PyPI
-        uses: pypa/gh-action-pypi-publish@release/v1
+name: Publish
+
+on:
+  workflow_dispatch:
+  release:
+    types: [created]
+
+jobs:
+  publish:
+    runs-on: ubuntu-latest
+    environment:
+      name: pypi
+      url: https://pypi.org/p/im2deep
+    permissions:
+      id-token: write
+    steps:
+      - uses: actions/checkout@v4
+
+      - name: Set up Python
+        uses: actions/setup-python@v4
+        with:
+          python-version: "3.8"
+
+      - name: Install dependencies
+        run: |
+          python -m pip install --upgrade pip build
+
+      - name: Build
+        run: python -m build
+
+      - name: Install
+        run: pip install dist/im2deep-*.whl
+
+      - name: Test package
+        run: |
+          im2deep --help
+
+      - name: Publish to PyPI
+        uses: pypa/gh-action-pypi-publish@release/v1

.gitignore

@@ -108,3 +108,6 @@ ENV/
 .vscode/
 .pytest_cache/
 IM2Deep.code-workspace
+
+# Testing
+test_data/

MANIFEST.in

@@ -1,3 +1,3 @@
-include im2deep/models/*
-include im2deep/models/**/*
-include im2deep/reference_data/*
+include im2deep/models/*
+include im2deep/models/**/*
+include im2deep/reference_data/*

README.md

@@ -1,46 +1,46 @@
-# IM2Deep
-Collisional cross-section prediction for (modified) peptides.
-
----
-## Introduction
-
-IM2Deep is a CCS predictor for (modified) peptides.
-It is able to accurately predict CCS for modified peptides, even if the modification wasn't observed during training.
-
-## Installation
-Install with pip:
-`pip install im2deep`
-
-## Usage
-### Basic CLI usage:
-```sh
-im2deep <path/to/peptide_file.csv>
-```
-If you want to calibrate your predictions (HIGHLY recommended), please provide a calibration file:
-```sh
-im2deep <path/to/peptide_file.csv> --calibration_file <path/to/peptide_file_with_CCS.csv>
-```
-For an overview of all CLI arguments, run `im2deep --help`.
-
-## Input files
-Both peptide and calibration files are expected to be comma-separated values (CSV) with the following columns:
-  - `seq`: unmodified peptide sequence
-  - `modifications`: every modifications should be listed as `location|name`, separated by a pipe character (`|`)
-     between the location, the name, and other modifications. `location` is an integer counted starting at 1 for the
-     first AA. 0 is reserved for N-terminal modifications, -1 for C-terminal modifications. `name` has to correspond
-     to a Unimod (PSI-MS) name.
-  - `charge`: peptide precursor charge
-  - `CCS`: collisional cross-section (only for calibration file)
-
-For example:
-
-```csv
-seq,modifications,charge,CCS
-VVDDFADITTPLK,,2,422.9984309464991
-GVEVLSLTPSFMDIPEK,12|Oxidation,2,464.6568644356109
-SYSGREFDDLSPTEQK,,2,468.9863221739147
-SYSQSILLDLTDNR,,2,460.9340710819608
-DEELIHLDGK,,2,383.8693416055445
-IPQEKCILQTDVK,5|Butyryl|6|Carbamidomethyl,3,516.2079366048176
-```
-
+# IM2Deep
+Collisional cross-section prediction for (modified) peptides.
+
+---
+## Introduction
+
+IM2Deep is a CCS predictor for (modified) peptides.
+It is able to accurately predict CCS for modified peptides, even if the modification wasn't observed during training.
+
+## Installation
+Install with pip:
+`pip install im2deep`
+
+## Usage
+### Basic CLI usage:
+```sh
+im2deep <path/to/peptide_file.csv>
+```
+If you want to calibrate your predictions (HIGHLY recommended), please provide a calibration file:
+```sh
+im2deep <path/to/peptide_file.csv> --calibration-file <path/to/peptide_file_with_CCS.csv>
+```
+For an overview of all CLI arguments, run `im2deep --help`.
+
+## Input files
+Both peptide and calibration files are expected to be comma-separated values (CSV) with the following columns:
+  - `seq`: unmodified peptide sequence
+  - `modifications`: every modifications should be listed as `location|name`, separated by a pipe character (`|`)
+     between the location, the name, and other modifications. `location` is an integer counted starting at 1 for the
+     first AA. 0 is reserved for N-terminal modifications, -1 for C-terminal modifications. `name` has to correspond
+     to a Unimod (PSI-MS) name.
+  - `charge`: peptide precursor charge
+  - `CCS`: collisional cross-section (only for calibration file)
+
+For example:
+
+```csv
+seq,modifications,charge,CCS
+VVDDFADITTPLK,,2,422.9984309464991
+GVEVLSLTPSFMDIPEK,12|Oxidation,2,464.6568644356109
+SYSGREFDDLSPTEQK,,2,468.9863221739147
+SYSQSILLDLTDNR,,2,460.9340710819608
+DEELIHLDGK,,2,383.8693416055445
+IPQEKCILQTDVK,5|Butyryl|6|Carbamidomethyl,3,516.2079366048176
+```
+

im2deep/__init__.py

@@ -1,3 +1,3 @@
-"""IM2Deep: Deep learning framework for peptide collisional cross section prediction."""
-
-__version__ = "0.1.7"
+"""IM2Deep: Deep learning framework for peptide collisional cross section prediction."""
+
+__version__ = "0.1.7"