Merge pull request #231 from MannLabs/develop

Develop
MannLabs · Oct 17, 2022 · 0f1275a · 0f1275a
2 parents a56f4a5 + e14e6a6
commit 0f1275a
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Showing 15 changed files with 38 additions and 23 deletions.
diff --git a/alphatims/__init__.py b/alphatims/__init__.py
@@ -2,7 +2,7 @@
 
 
 __project__ = "alphatims"
-__version__ = "1.0.4"
+__version__ = "1.0.5"
 __license__ = "Apache"
 __description__ = "A Python package to index Bruker TimsTOF raw data for fast and easy accession and visualization"
 __author__ = "Sander Willems, Eugenia Voytik"
@@ -17,14 +17,15 @@
     "bioinformatics",
     "data indexing",
 ]
-__python_version__ = ">=3.8,<3.10"
+__python_version__ = ">=3.8,<4"
 __classifiers__ = [
     "Development Status :: 5 - Production/Stable",
     "Intended Audience :: Science/Research",
     "License :: OSI Approved :: Apache Software License",
     "Operating System :: OS Independent",
     "Programming Language :: Python :: 3.8",
     "Programming Language :: Python :: 3.9",
+    "Programming Language :: Python :: 3.10",
     "Topic :: Scientific/Engineering :: Bio-Informatics",
 ]
 __console_scripts__ = [

diff --git a/alphatims/bruker.py b/alphatims/bruker.py
@@ -306,7 +306,7 @@ def parse_decompressed_bruker_binary_type2(decompressed_bytes: bytes) -> tuple:
     last_scan = len(intensities) - np.sum(scan_indices[1:])
     scan_indices[:-1] = scan_indices[1:]
     scan_indices[-1] = last_scan
-    return scan_indices, tof_indices, intensities
+    return scan_indices, tof_indices - 1, intensities
 
 
 @alphatims.utils.njit(nogil=True)

diff --git a/alphatims/tempmmap.py b/alphatims/tempmmap.py
@@ -221,8 +221,16 @@ def reset() -> str:
             f"Folder {TEMP_DIR_NAME} with temp mmap arrays is being deleted. "
             "All existing temp mmapp arrays will be unusable!"
         )
-    for _array in ARRAYS.values():
-        _array[1].close()
+    import gc
+    for _array_name in list(ARRAYS.keys()):
+        _array_tuple = ARRAYS.pop(_array_name)
+        _array, _memmap = _array_tuple
+        del _array_tuple
+        _array.data.release()
+        del _array
+        gc.collect()
+        _memmap.close()
+        del _memmap
     del _TEMP_DIR
     _TEMP_DIR, TEMP_DIR_NAME = make_temp_dir()
     ARRAYS = {}

diff --git a/alphatims/utils.py b/alphatims/utils.py
@@ -621,16 +621,20 @@ def wrapper(iterable, *args):
                 threads.append(thread)
             if include_progress_callback:
                 import time
+                if len(iterable) > 10**6:
+                    granularity = 1000
+                else:
+                    granularity = len(iterable)
                 # progress_count = 0
                 progress_bar = 0
                 progress_count = np.sum(progress_counter)
                 for result in progress_callback(
-                    iterable,
+                    range(granularity),
                     include_progress_callback=include_progress_callback
                 ):
                     while progress_bar >= progress_count:
                         time.sleep(0.01)
-                        progress_count = np.sum(progress_counter)
+                        progress_count = granularity * np.sum(progress_counter) / len(iterable)
                     progress_bar += 1
             for thread in threads:
                 thread.join()

diff --git a/misc/bumpversion.cfg b/misc/bumpversion.cfg
@@ -1,5 +1,5 @@
 [bumpversion]
-current_version = 1.0.4
+current_version = 1.0.5
 commit = True
 tag = False
 parse = (?P<major>\d+)\.(?P<minor>\d+)\.(?P<patch>\d+)(\-(?P<release>[a-z]+)(?P<build>\d+))?

diff --git a/misc/one_click_linux/control b/misc/one_click_linux/control
@@ -1,5 +1,5 @@
 Package: AlphaTims
-Version: 1.0.4
+Version: 1.0.5
 Architecture: all
 Maintainer: Mann Labs <[email protected]>
 Description: AlphaTims GUI

diff --git a/misc/one_click_linux/create_installer_linux.sh b/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-1.0.4-py3-none-any.whl[plotting-stable,stable,legacy-stable]"
+pip install "../../dist/alphatims-1.0.5-py3-none-any.whl[plotting-stable,stable,legacy-stable]"
 pip install pyinstaller==4.10
 pyinstaller ../pyinstaller/alphatims.spec -y
 conda deactivate

diff --git a/misc/one_click_macos/Info.plist b/misc/one_click_macos/Info.plist
@@ -9,9 +9,9 @@
 	<key>CFBundleIconFile</key>
 	<string>alpha_logo.icns</string>
 	<key>CFBundleIdentifier</key>
-	<string>alphatims.1.0.4</string>
+	<string>alphatims.1.0.5</string>
 	<key>CFBundleShortVersionString</key>
-	<string>1.0.4</string>
+	<string>1.0.5</string>
 	<key>CFBundleInfoDictionaryVersion</key>
 	<string>6.0</string>
 	<key>CFBundleName</key>

diff --git a/misc/one_click_macos/create_installer_macos.sh b/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-1.0.4-py3-none-any.whl[plotting-stable,stable,legacy-stable]"
+pip install "../../dist/alphatims-1.0.5-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)" $f; done
   codesign --sign "Developer ID Application: Max-Planck-Gesellschaft zur Förderung der Wissenschaften e.V. (7QSY5527AQ)" dist/alphatims/Contents/MacOS/alphatims_gui --force --options=runtime --entitlements entitlements.xml
-  pkgbuild --root dist/alphatims --identifier de.mpg.biochem.alphatims.app --version 1.0.4 --install-location /Applications/AlphaTims.app --scripts scripts alphatims.pkg --sign "Developer ID Installer: Max-Planck-Gesellschaft zur Förderung der Wissenschaften e.V. (7QSY5527AQ)"
+  pkgbuild --root dist/alphatims --identifier de.mpg.biochem.alphatims.app --version 1.0.5 --install-location /Applications/AlphaTims.app --scripts scripts alphatims.pkg --sign "Developer ID Installer: Max-Planck-Gesellschaft zur Förderung der Wissenschaften e.V. (7QSY5527AQ)"
   productbuild --distribution distribution.xml --resources Resources --package-path alphatims.pkg dist/alphatims_gui_installer_macos.pkg --sign "Developer ID Installer: Max-Planck-Gesellschaft zur Förderung der Wissenschaften e.V. (7QSY5527AQ)"
   requestUUID=$(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 1.0.4 --install-location /Applications/AlphaTims.app --scripts scripts alphatims.pkg
+  pkgbuild --root dist/alphatims --identifier de.mpg.biochem.alphatims.app --version 1.0.5 --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
diff --git a/misc/one_click_macos/distribution.xml b/misc/one_click_macos/distribution.xml
@@ -1,6 +1,6 @@
 <?xml version="1.0" encoding="utf-8" standalone="no"?>
 <installer-script minSpecVersion="1.000000">
-    <title>AlphaTims 1.0.4</title>
+    <title>AlphaTims 1.0.5</title>
     <background mime-type="image/png" file="alpha_logo.png" scaling="proportional"/>
     <welcome file="welcome.html" mime-type="text/html" />
     <conclusion file="conclusion.html" mime-type="text/html" />

diff --git a/misc/one_click_windows/alphatims_innoinstaller.iss b/misc/one_click_windows/alphatims_innoinstaller.iss
@@ -2,7 +2,7 @@
 ; SEE THE DOCUMENTATION FOR DETAILS ON CREATING INNO SETUP SCRIPT FILES!
 
 #define MyAppName "AlphaTims"
-#define MyAppVersion "1.0.4"
+#define MyAppVersion "1.0.5"
 #define MyAppPublisher "Max Planck Institute of Biochemistry, Mann department"
 #define MyAppURL "https://github.com/MannLabs/alphatims"
 #define MyAppExeName "alphatims_gui.exe"

diff --git a/misc/one_click_windows/create_installer_windows.bat b/misc/one_click_windows/create_installer_windows.bat
@@ -15,7 +15,7 @@ call rmdir dist /s /q
 call rmdir build /s /q
 call python setup.py sdist bdist_wheel
 call cd misc/one_click_windows
-call pip install "../../dist/alphatims-1.0.4-py3-none-any.whl[plotting-stable,stable,legacy-stable]"
+call pip install "../../dist/alphatims-1.0.5-py3-none-any.whl[plotting-stable,stable,legacy-stable]"
 call pip install pyinstaller==4.10
 call pyinstaller ../pyinstaller/alphatims.spec -y
 call conda deactivate

diff --git a/misc/one_click_windows/create_installer_windows.sh b/misc/one_click_windows/create_installer_windows.sh
@@ -7,7 +7,7 @@ rm -rf dist
 rm -rf build
 python setup.py sdist bdist_wheel
 cd misc/one_click_windows
-pip install "../../dist/alphatims-1.0.4-py3-none-any.whl[plotting-stable,stable,legacy-stable]"
+pip install "../../dist/alphatims-1.0.5-py3-none-any.whl[plotting-stable,stable,legacy-stable]"
 pip install pyinstaller==4.10
 # TODO https://stackoverflow.com/questions/54175042/python-3-7-anaconda-environment-import-ssl-dll-load-fail-error/60405693#60405693
 pyinstaller ../pyinstaller/alphatims.spec -y

diff --git a/requirements/requirements_development.txt b/requirements/requirements_development.txt
@@ -7,3 +7,5 @@ plotly==4.12.0
 seaborn==0.11.0
 twine==4.0.0
 bumpversion==0.6.0
+
+pywin32; sys_platform=='win32'
diff --git a/setup.py b/setup.py
@@ -21,8 +21,11 @@
         extra_requirements[extra] = []
         for line in requirements_file:
             extra_requirements[extra_stable].append(line)
+            # conditional req like: "pywin32; sys_platform=='win32'"
+            line, *conditions = line.split(';')
             requirement, *comparison = re.split("[><=~!]", line)
             requirement == requirement.strip()
+            requirement = ";".join([requirement] + conditions)
             extra_requirements[extra].append(requirement)
 
 requirements = extra_requirements.pop("")
@@ -45,10 +48,7 @@
     entry_points={
         "console_scripts": package2install.__console_scripts__,
     },
-    install_requires=requirements + [
-        # TODO Remove hardcoded requirement?
-        "pywin32==225; sys_platform=='win32'"
-    ],
+    install_requires=requirements,
     extras_require=extra_requirements,
     python_requires=package2install.__python_version__,
 )