Merge pull request #276 from MannLabs/development

release 1.7.2
MannLabs · Jul 15, 2024 · 6e27ebc · 6e27ebc
2 parents 46f6190 + 148857e
commit 6e27ebc
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Showing 32 changed files with 379 additions and 1,690 deletions.
diff --git a/.github/workflows/e2e_testing.yml b/.github/workflows/e2e_testing.yml
@@ -21,6 +21,9 @@ jobs:
       BRANCH_NAME: ${{ github.head_ref || github.ref_name }}
       NEPTUNE_API_TOKEN: ${{ secrets.NEPTUNE_E2E_TOKEN }}
       NEPTUNE_PROJECT_NAME: "MannLabs/alphaDIA-e2e-tests"
+      NUMBA_BOUNDSCHECK: 1
+      NUMBA_DEVELOPER_MODE: 1
+      NUMBA_FULL_TRACEBACKS: 1
     steps:
       - uses: actions/checkout@v4
       - name: Conda info
@@ -41,9 +44,9 @@ jobs:
         if: always()
         shell: bash -el {0}
         run: |
-          conda remove -n $RUN_NAME --all
+          conda remove -n $RUN_NAME --all -y
       - name: Delete Caches on Error
-        if: steps.pip_installation.outcome == 'failure'
+        if: ${{ failure() && steps.pip_installation.conclusion == 'failure' }}
         run: |
           rm -rf ~/.cache/pip
           rm -rf ~/.cache/conda
diff --git a/README.md b/README.md
@@ -1,10 +1,12 @@
-![Release](https://img.shields.io/badge/release-v1.6.0-brightgreen)
+![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)
 ![License](https://img.shields.io/badge/License-Apache-brightgreen)
-![Tests](https://github.com/MannLabs/alphadia/workflows/Default%20installation%20and%20tests/badge.svg)
+![GitHub Actions Workflow Status](https://img.shields.io/github/actions/workflow/status/mannlabs/alphadia/e2e_testing.yml?branch=main&label=E2E%20Tests)
+![GitHub Actions Workflow Status](https://img.shields.io/github/actions/workflow/status/mannlabs/alphadia/pip_installation.yml?branch=main&label=Unit%20Tests)
 ![Docs](https://readthedocs.org/projects/alphadia/badge/?version=latest)
-![Deployment](https://github.com/MannLabs/alphadia/workflows/Publish%20on%20PyPi%20and%20release%20on%20GitHub/badge.svg)
+![GitHub Actions Workflow Status](https://img.shields.io/github/actions/workflow/status/mannlabs/alphadia/publish_docker_image.yml?branch=main&label=Deploy%20Docker)
+![GitHub Actions Workflow Status](https://img.shields.io/github/actions/workflow/status/mannlabs/alphadia/publish_on_pypi.yml?branch=main&label=Deploy%20PyPi)
 ![Coverage](https://github.com/MannLabs/alphadia/blob/main/coverage.svg)
-![Versions](https://img.shields.io/badge/python-3.10_%7C_3.11_%7C_3.12-green)
 
 <!-- PROJECT LOGO -->
 <br />

diff --git a/alphadia/__init__.py b/alphadia/__init__.py
@@ -1,3 +1,3 @@
 #!python
 
-__version__ = "1.7.1"
+__version__ = "1.7.2"
diff --git a/alphadia/data/bruker.py b/alphadia/data/bruker.py
@@ -1,21 +1,15 @@
-# native imports
 import logging
 import math
 import os
 
 import alphatims.bruker
 import alphatims.tempmmap as tm
-
-# alpha family imports
 import alphatims.utils
 import numba as nb
-
-# third party imports
 import numpy as np
 from numba.core import types
 from numba.experimental import jitclass
 
-# alphadia imports
 from alphadia import utils
 from alphadia.data.stats import log_stats
 
@@ -65,23 +59,30 @@ def __init__(
                     mmap_detector_events,
                 )
 
-                if self._cycle.shape[0] != 1:
+                try:
+                    cycle_shape = self._cycle.shape[0]
+                except AttributeError as e:
                     logger.error(
-                        "Unexpected cycle shape. Will only retain first frame group"
-                    )
-                    raise ValueError(
-                        "Unexpected cycle shape. Will only retain first frame group"
+                        "Could not find cycle shape. Please check if this is a valid DIA data set."
                     )
+                    raise e
+                else:
+                    if cycle_shape != 1:
+                        msg = f"Unexpected cycle shape: {cycle_shape} (expected: 1). "
+                        logger.error(msg)
+                        raise ValueError(msg)
 
                 self.transpose()
+
         elif bruker_d_folder_name.endswith(".hdf"):
             self._import_data_from_hdf_file(
                 bruker_d_folder_name,
                 mmap_detector_events,
             )
             self.bruker_hdf_file_name = bruker_d_folder_name
         else:
-            raise NotImplementedError("WARNING: file extension not understood")
+            raise NotImplementedError("ERROR: file extension not understood")
+
         if not hasattr(self, "version"):
             self._version = "N.A."
         if self.version != alphatims.__version__: