Updates for publish workflow

.github/workflows/publish.yml

@@ -0,0 +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

.gitignore

@@ -107,3 +107,4 @@ ENV/
 # vscode
 .vscode/
 .pytest_cache/
+IM2Deep.code-workspace

MANIFEST.in

@@ -1,2 +1,2 @@
-include im2deep/models/*
-include im2deep/reference_data/*
+include im2deep/models/**/*
+include im2deep/reference_data/**/*

im2deep/__main__.py

@@ -110,7 +110,6 @@ def main(
     """Command line interface to IM2Deep."""
     setup_logging(log_level)
     try:
-        #TODO: Add other arguments like calibrate_per_charge, use_charge_state, n_jobs
         run(psm_file, calibration_file, output_file, model_name, calibrate_per_charge, use_charge_state, n_jobs)
     except IM2DeepError as e:
         LOGGER.error(e)
@@ -137,7 +136,6 @@ def run(
         # Read input file
         df_pred = pd.read_csv(file_pred)
         df_pred.fillna("", inplace=True)
-        del file_pred
 
         list_of_psms = []
         for seq, mod, charge, ident in zip(
@@ -215,6 +213,20 @@ def run(
         ):
             file_pred_out.write(f"{seq},{mod},{charge},{CCS}\n")
         file_pred_out.close()
+    else:
+        file_pred_out_path = Path(file_pred)
+        file_pred_out_path.with_stem(file_pred_out_path.stem + "_predictions")
+        file_pred_out = open(file_pred_out_path, "w")
+        file_pred_out.write("seq,modifications,charge,predicted CCS\n")
+        for seq, mod, charge, ident, CCS in zip(
+            df_pred["seq"],
+            df_pred["modifications"],
+            df_pred["charge"],
+            df_pred.index,
+            calibrated_psm_list_pred_df["predicted_ccs_calibrated"],
+        ):
+            file_pred_out.write(f"{seq},{mod},{charge},{CCS}\n")
+        file_pred_out.close()
 
     LOGGER.info("IM2Deep finished!")
 

pyproject.toml

@@ -23,7 +23,10 @@ dependencies = [
     "deeplc",
     "deeplcretrainer",
     "psm_utils",
-    "tensorflow>=2.2,<2.13.0"
+    "tensorflow>=2.2,<2.13.0",
+    "pandas",
+    "numpy",
+    "rich"
 ]
 
 [project.optional-dependencies]
@@ -50,6 +53,9 @@ im2deep = "im2deep.__main__:main"
 requires = ["setuptools"]
 build-backend = "setuptools.build_meta"
 
+[tool.setuptools.dynamic]
+version = {attr = "im2deep.__version__"}
+
 [tool.isort]
 profile = "black"