Merge pull request #225 from MannLabs/develop

Develop

Author: sander-willems-bruker

alphatims/__init__.py

@@ -2,7 +2,7 @@
 
 
 __project__ = "alphatims"
-__version__ = "1.0.2"
+__version__ = "1.0.3"
 __license__ = "Apache"
 __description__ = "A Python package to index Bruker TimsTOF raw data for fast and easy accession and visualization"
 __author__ = "Sander Willems, Eugenia Voytik"

alphatims/bruker.py

@@ -249,6 +249,7 @@ def read_bruker_sql(
             frames.MaxIntensity[0] = 0
             frames.SummedIntensities[0] = 0
             frames.NumPeaks[0] = 0
+            frames.MsMsType[0] = 0
         polarity_col = frames["Polarity"].copy()
         frames = pd.DataFrame(
             {
@@ -1183,7 +1184,8 @@ def _import_data_from_d_folder(
         self._parse_quad_indptr()
         self._intensity_min_value = int(np.min(self.intensity_values))
         self._intensity_max_value = int(np.max(self.intensity_values))
-        self.set_cycle()
+        if self.acquisition_mode == "diaPASEF":
+            self.set_cycle()
 
     def save_as_hdf(
         self,
@@ -2273,19 +2275,13 @@ def use_calibrated_mz_values_as_default(
     def set_cycle(self) -> None:
         """Set the quad cycle for diaPASEF data.
         """
-        last_window_group = -1
-        for max_index, (frame, window_group) in enumerate(
-            zip(
-                self.fragment_frames.Frame,
-                self.fragment_frames.Precursor
-            )
-        ):
-            if window_group < last_window_group:
+        subframes = self.fragment_frames.drop("Frame", axis=1)
+        for max_index in range(1, len(subframes)):
+            subframe = subframes.iloc[max_index]
+            if subframe.equals(subframes.iloc[0]):
                 break
-            else:
-                last_window_group = window_group
-        frames = self.fragment_frames.Frame[max_index-1]
-        frames += self.fragment_frames.Frame[0] == int(self.zeroth_frame)
+        frames = self.fragment_frames.Frame[max_index] - 1
+        frames += (1 - int(self.zeroth_frame))
         sub_cycles = frames - len(np.unique(self.fragment_frames.Frame[:max_index]))
         cycle = np.zeros(
             (

alphatims/cli.py

@@ -269,7 +269,10 @@ def detect(**kwargs):
 def export_hdf(**kwargs):
     with parse_cli_settings("export hdf", **kwargs) as parameters:
         import alphatims.bruker
-        data = alphatims.bruker.TimsTOF(parameters["bruker_raw_data"])
+        data = alphatims.bruker.TimsTOF(
+            parameters["bruker_raw_data"],
+            use_hdf_if_available=False
+        )
         if "output_folder" not in parameters:
             directory = data.directory
         else:

alphatims/plotting.py

@@ -129,7 +129,7 @@ def line_plot(
 
 def heatmap(
     df,
-    x_axis_label: str = "rt",
+    x_axis_label: str = "mz",
     y_axis_label: str = "mobility",
     title: str = "",
     z_axis_label: str = "intensity",

alphatims/tempmmap.py

@@ -40,7 +40,7 @@ def make_temp_dir(prefix: str = "temp_mmap_") -> tuple:
     f"WARNING: Temp mmap arrays are written to {TEMP_DIR_NAME}. "
     "Cleanup of this folder is OS dependant, "
     "and might need to be triggered manually! "
-    f"Current space: {shutil.disk_usage(TEMP_DIR_NAME)[-1]}"
+    f"Current space: {shutil.disk_usage(TEMP_DIR_NAME)[-1]:,}"
 )
 
 

misc/bumpversion.cfg

@@ -1,5 +1,5 @@
 [bumpversion]
-current_version = 1.0.2
+current_version = 1.0.3
 commit = True
 tag = False
 parse = (?P<major>\d+)\.(?P<minor>\d+)\.(?P<patch>\d+)(\-(?P<release>[a-z]+)(?P<build>\d+))?

misc/one_click_linux/control

@@ -1,5 +1,5 @@
 Package: AlphaTims
-Version: 1.0.2
+Version: 1.0.3
 Architecture: all
 Maintainer: Mann Labs <[email protected]>
 Description: AlphaTims GUI

misc/one_click_linux/create_installer_linux.sh

@@ -12,7 +12,7 @@ rm -rf dist
 rm -rf build
 python setup.py sdist bdist_wheel
 cd misc/one_click_linux
-pip install "../../dist/alphatims-1.0.2-py3-none-any.whl[plotting-stable,stable,legacy-stable]"
+pip install "../../dist/alphatims-1.0.3-py3-none-any.whl[plotting-stable,stable,legacy-stable]"
 pip install pyinstaller==4.10
 pyinstaller ../pyinstaller/alphatims.spec -y
 conda deactivate

misc/one_click_macos/Info.plist

@@ -9,9 +9,9 @@
 	<key>CFBundleIconFile</key>
 	<string>alpha_logo.icns</string>
 	<key>CFBundleIdentifier</key>
-	<string>alphatims.1.0.2</string>
+	<string>alphatims.1.0.3</string>
 	<key>CFBundleShortVersionString</key>
-	<string>1.0.2</string>
+	<string>1.0.3</string>
 	<key>CFBundleInfoDictionaryVersion</key>
 	<string>6.0</string>
 	<key>CFBundleName</key>

misc/one_click_macos/create_installer_macos.sh

@@ -17,7 +17,7 @@ rm -rf build
 python setup.py sdist bdist_wheel
 cd misc/one_click_macos
 pip install pyinstaller==4.10
-pip install "../../dist/alphatims-1.0.2-py3-none-any.whl[plotting-stable,stable,legacy-stable]"
+pip install "../../dist/alphatims-1.0.3-py3-none-any.whl[plotting-stable,stable,legacy-stable]"
 conda list
 pyinstaller ../pyinstaller/alphatims.spec -y
 conda deactivate
@@ -34,7 +34,7 @@ if false; then
   # https://scriptingosx.com/2019/09/notarize-a-command-line-tool/
   for f in $(find dist/alphatims -name '*.so' -or -name '*.dylib'); do codesign --sign "Developer ID Application: Max-Planck-Gesellschaft zur Förderung der Wissenschaften e.V. (7QSY5527AQ)" $f; done
   codesign --sign "Developer ID Application: Max-Planck-Gesellschaft zur Förderung der Wissenschaften e.V. (7QSY5527AQ)" dist/alphatims/Contents/MacOS/alphatims_gui --force --options=runtime --entitlements entitlements.xml
-  pkgbuild --root dist/alphatims --identifier de.mpg.biochem.alphatims.app --version 1.0.2 --install-location /Applications/AlphaTims.app --scripts scripts alphatims.pkg --sign "Developer ID Installer: Max-Planck-Gesellschaft zur Förderung der Wissenschaften e.V. (7QSY5527AQ)"
+  pkgbuild --root dist/alphatims --identifier de.mpg.biochem.alphatims.app --version 1.0.3 --install-location /Applications/AlphaTims.app --scripts scripts alphatims.pkg --sign "Developer ID Installer: Max-Planck-Gesellschaft zur Förderung der Wissenschaften e.V. (7QSY5527AQ)"
   productbuild --distribution distribution.xml --resources Resources --package-path alphatims.pkg dist/alphatims_gui_installer_macos.pkg --sign "Developer ID Installer: Max-Planck-Gesellschaft zur Förderung der Wissenschaften e.V. (7QSY5527AQ)"
   requestUUID=$(xcrun altool --notarize-app --primary-bundle-id "de.mpg.biochem.alphatims.app" --username "[email protected]" --password "@keychain:Alphatims-develop" --asc-provider 7QSY5527AQ --file dist/alphatims_gui_installer_macos.pkg 2>&1 | awk '/RequestUUID/ { print $NF; }')
   request_status="in progress"
@@ -46,6 +46,6 @@ if false; then
   xcrun altool --notarization-info "$requestUUID" --username "[email protected]" --password "@keychain:Alphatims-develop"
   xcrun stapler staple dist/alphatims_gui_installer_macos.pkg
 else
-  pkgbuild --root dist/alphatims --identifier de.mpg.biochem.alphatims.app --version 1.0.2 --install-location /Applications/AlphaTims.app --scripts scripts alphatims.pkg
+  pkgbuild --root dist/alphatims --identifier de.mpg.biochem.alphatims.app --version 1.0.3 --install-location /Applications/AlphaTims.app --scripts scripts alphatims.pkg
   productbuild --distribution distribution.xml --resources Resources --package-path alphatims.pkg dist/alphatims_gui_installer_macos.pkg
 fi