Merge pull request #115 from MannLabs/develop

Develop
MannLabs · Apr 23, 2021 · f9d405e · f9d405e
2 parents 1b6aa0b + c10312b
commit f9d405e
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diff --git a/.github/workflows/version_check.yml b/.github/workflows/version_check.yml
@@ -13,7 +13,7 @@ jobs:
       - name: Master version bumped
         shell: bash -l {0}
         run: |
-          current_version=$(grep "__version__" alphatims/__init__.py | cut -f3 -d ' ')
+          current_version=$(grep "__version__" alphatims/__init__.py | cut -f3 -d ' ' | sed 's/"//g')
           github_version=$(curl "https://raw.githubusercontent.com/MannLabs/alphatims/master/alphatims/__init__.py" | grep "__version__" | cut -f3 -d ' ')
           if [ "$current_version" = "$github_version" ]; then
             echo "Version is not updated"
@@ -22,8 +22,8 @@ jobs:
       - name: Tutorial notebook updated
         shell: bash -l {0}
         run: |
-          current_version=$(grep "__version__" alphatims/__init__.py | cut -f3 -d ' ')
-          tutorial_version=(grep "alphatims" nbs/tutorial_log.txt | head -n 1 | tr -s ' ' | cut -d ' ' -f5)
+          current_version=$(grep "__version__" alphatims/__init__.py | cut -f3 -d ' ' | sed 's/"//g')
+          tutorial_version=$(grep "alphatims" nbs/tutorial_log.txt | head -n 1 | tr -s ' ' | cut -d ' ' -f5)
           if [ "$current_version" != "$tutorial_version" ]; then
             echo "Version is not updated"
             echo "current: $current_version new: $tutorial_version"
@@ -32,22 +32,23 @@ jobs:
       - name: Performance notebook updated
         shell: bash -l {0}
         run: |
-          current_version=$(grep "__version__" alphatims/__init__.py | cut -f3 -d ' ')
-          performance_version=(grep "alphatims" nbs/performance_log.txt | head -n 1 | tr -s ' ' | cut -d ' ' -f5)
+          current_version=$(grep "__version__" alphatims/__init__.py | cut -f3 -d ' ' | sed 's/"//g')
+          performance_version=$(grep "alphatims" nbs/performance_log.txt | head -n 1 | tr -s ' ' | cut -d ' ' -f5)
           if [ "$current_version" != "$performance_version" ]; then
             echo "Version is not updated"
             echo "current: $current_version new: $performance_version"
             exit 1
           fi
-      - name: Readme performance updated
+      - name: Readme updated
         shell: bash -l {0}
         run: |
-          echo "TODO check if readme performance equals performance notebook"
+          echo "Make sure the readme is updated"
       - name: GUI_manual.pdf updated
         shell: bash -l {0}
         run: |
+          echo "make sure the GUI_manual.pdf is updated"
           # TODO git does not preserve timestamps, so following is impossible
-          if [ misc/gui_manual.docx -nt alphatims/docs/gui_manual.pdf ]; then
-            echo "GUI manual was not updated"
-            exit 1
-          fi
+          # if [ misc/gui_manual.docx -nt alphatims/docs/gui_manual.pdf ]; then
+          #   echo "GUI manual was not updated"
+          #   exit 1
+          # fi
diff --git a/README.md b/README.md
@@ -1,5 +1,5 @@
 ![Pip installation](https://github.com/MannLabs/alphatims/workflows/Default%20installation%20and%20tests/badge.svg)
-![GUI and PyPi releases](https://github.com/MannLabs/alphatims/workflows/Create%20all%20GUI%20releases%20and%20publish%20on%20PyPi/badge.svg)
+![GUI and PyPi releases](https://github.com/MannLabs/alphatims/workflows/Publish%20on%20PyPi%20and%20release%20on%20GitHub/badge.svg)
 
 ---
 # AlphaTims
@@ -248,32 +248,7 @@ Performance can be measured in function of [speed](#speed) or [RAM](#ram) usage.
 
 ### Speed
 
-Typical time performance statistics on data in-/output and slicing of standard [HeLa datasets](#test-sample) include:
-
-| type | gradient | datapoints    | reading (raw/HDF) | export HDF| slicing (in ms)         |
-|------|----------|---------------|-------------------|--------|----------------------------|
-| DDA  | 6 min    | 214,172,697   | 1.48 s / 445 ms   | 569 ms | 1.85 / 48 / 27.1 / 89.7  |
-| DIA  | 6 min    | 158,552,099   | 1.06 s / 295 ms   | 409 ms | 7.35 / 24.1 / 649 / 110    |
-| DDA  | 21 min   | 295,251,252   | 3.07 s / 755 ms   | 779 ms | 2.17 / 68.3 / 106 / 181    |
-| DIA  | 21 min   | 730,564,765   | 5.24 s / 1.90 s   | 1.79 s | 0.860 / 123 / 4910 / 392    |
-| DDA  | 120 min  | 2,074,019,899 | 23.2 s / 10.1 s   | 4.94 s | 0.671 / 338 / 557 / 1100   |
-
-All slices were performed in a single dimension. Including more slices makes the analysis more stringent and hence faster. The considered dimensions were:
-
-* **LC:** 100.0 <= retention_time < 100.5
-* **TIMS:** scan_index = 450
-* **Quadrupole:** 700.0 <= quad_mz_values < 710.0
-* **TOF:** 621.9 <= tof_mz_values < 622.1
-
-All of these analyses were timed with `timeit` and are the average of at least 7 runs. They were obtained on the following system:
-
-* **MacBook Pro:** 13-inch, 2020, Four Thunderbolt 3 ports
-* **OS version:** macOS Catalina 10.15.7
-* **Processor:** 2.3 GHz Quad-Core Intel Core i7
-* **Memory:** 32 GB 3733 MHz LPDDR4X
-* **Startup Disk:** Macintosh HD
-
-Full details are available in the [performance notebook](nbs/performance.ipynb).
+Typical time performance statistics on data in-/output and slicing of standard [HeLa datasets](#test-sample) are available in the [performance notebook](nbs/performance.ipynb).
 
 ### RAM
 

diff --git a/alphatims/__init__.py b/alphatims/__init__.py
@@ -2,7 +2,7 @@
 
 
 __project__ = "alphatims"
-__version__ = "0.2.4"
+__version__ = "0.2.5"
 __license__ = "Apache"
 __description__ = "A Python package to index Bruker TimsTOF raw data for fast and easy accession and visualization"
 __author__ = "Sander Willems, Eugenia Voytik"

diff --git a/alphatims/utils.py b/alphatims/utils.py
@@ -126,31 +126,33 @@ def show_platform_info() -> None:
     This is done in the following format:
 
         - [timestamp]> Platform information:
-        - [timestamp]> system     - [...]
-        - [timestamp]> release    - [...]
-        - [timestamp]> version    - [...]
-        - [timestamp]> machine    - [...]
-        - [timestamp]> processor  - [...]
-        - [timestamp]> cpu count  - [...]
-        - [timestamp]> ram        - [...]/[...] Gb (available/total)
+        - [timestamp]> system         - [...]
+        - [timestamp]> release        - [...]
+        - [timestamp]> version        - [...]
+        - [timestamp]> machine        - [...]
+        - [timestamp]> processor      - [...]
+        - [timestamp]> cpu count      - [...]
+        - [timestamp]> cpu frequency  - [...]
+        - [timestamp]> ram            - [...]/[...] Gb (available/total)
     """
     import platform
     import psutil
     logging.info("Platform information:")
-    logging.info(f"system     - {platform.system()}")
-    logging.info(f"release    - {platform.release()}")
+    logging.info(f"system        - {platform.system()}")
+    logging.info(f"release       - {platform.release()}")
     if platform.system() == "Darwin":
-        logging.info(f"version    - {platform.mac_ver()[0]}")
+        logging.info(f"version       - {platform.mac_ver()[0]}")
     else:
-        logging.info(f"version    - {platform.version()}")
-    logging.info(f"machine    - {platform.machine()}")
-    logging.info(f"processor  - {platform.processor()}")
+        logging.info(f"version       - {platform.version()}")
+    logging.info(f"machine       - {platform.machine()}")
+    logging.info(f"processor     - {platform.processor()}")
     logging.info(
-        f"cpu count  - {psutil.cpu_count()}"
+        f"cpu count     - {psutil.cpu_count()}"
         # f" ({100 - psutil.cpu_percent()}% unused)"
     )
+    logging.info(f"cpu frequency - {psutil.cpu_freq().current:.2f} Mhz")
     logging.info(
-        f"ram        - "
+        f"ram           - "
         f"{psutil.virtual_memory().available/1024**3:.1f}/"
         f"{psutil.virtual_memory().total/1024**3:.1f} Gb "
         f"(available/total)"

diff --git a/misc/bumpversion.cfg b/misc/bumpversion.cfg
@@ -1,5 +1,5 @@
 [bumpversion]
-current_version = 0.2.4
+current_version = 0.2.5
 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/checklist.txt b/misc/checklist.txt
@@ -1,16 +1,26 @@
 ######## ALWAYS TODO ########
 
 Versions updated
+  conda activate alphatims
   cd misc
-  # bumpversion patch --new-version VERSION --config-file bumpversion.cfg
   bumpversion patch --config-file bumpversion.cfg
+  conda deactivate
+  # bumpversion patch --new-version VERSION --config-file bumpversion.cfg
 
 No TODOs left?
 
-Tutorial/manual/performance/README updated?
-  jupyter nbconvert --execute --to notebook --NotebookClient.kernel_name="python" nbs/tutorial.ipynb nbs/performance.ipynb
+README updated?
 
+Manual updated?
+  if [ misc/gui_manual.docx -nt alphatims/docs/gui_manual.pdf ]; then
+   echo "GUI manual was not updated"
+  fi
 
+Tutorial and performance?
+  conda activate alphatims
+  jupyter nbconvert --execute --inplace --to notebook --NotebookClient.kernel_name="python" nbs/tutorial.ipynb nbs/performance.ipynb
+  jupyter nbconvert --to html --NotebookClient.kernel_name="python" nbs/tutorial.ipynb nbs/performance.ipynb
+  conda deactivate
 
 
 

diff --git a/misc/one_click_linux/control b/misc/one_click_linux/control
@@ -1,5 +1,5 @@
 Package: AlphaTims
-Version: 0.2.4
+Version: 0.2.5
 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-0.2.4-py3-none-any.whl[plotting]"
+pip install "../../dist/alphatims-0.2.5-py3-none-any.whl[plotting]"
 pip install pyinstaller==4.2
 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.0.2.4</string>
+	<string>alphatims.0.2.5</string>
 	<key>CFBundleShortVersionString</key>
-	<string>0.2.4</string>
+	<string>0.2.5</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==4.2
-pip install "../../dist/alphatims-0.2.4-py3-none-any.whl[plotting]"
+pip install "../../dist/alphatims-0.2.5-py3-none-any.whl[plotting]"
 conda list
 pyinstaller ../pyinstaller/alphatims.spec -y
 conda deactivate
@@ -33,7 +33,7 @@ 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)" $f; done
   codesign --sign "Developer ID Application: Max-Planck-Gesellschaft zur Förderung der Wissenschaften e.V. (7QSY5527AQ)" dist/alphatims/Contents/MacOS/alphatims_gui --force --options=runtime --entitlements entitlements.xml
-  pkgbuild --root dist/alphatims --identifier de.mpg.biochem.alphatims.app --version 0.2.4 --install-location /Applications/AlphaTims.app --scripts scripts alphatims.pkg --sign "Developer ID Installer: Max-Planck-Gesellschaft zur Förderung der Wissenschaften e.V. (7QSY5527AQ)"
+  pkgbuild --root dist/alphatims --identifier de.mpg.biochem.alphatims.app --version 0.2.5 --install-location /Applications/AlphaTims.app --scripts scripts alphatims.pkg --sign "Developer ID Installer: Max-Planck-Gesellschaft zur Förderung der Wissenschaften e.V. (7QSY5527AQ)"
   productbuild --distribution distribution.xml --resources Resources --package-path alphatims.pkg dist/alphatims_gui_installer_macos.pkg --sign "Developer ID Installer: Max-Planck-Gesellschaft zur Förderung der Wissenschaften e.V. (7QSY5527AQ)"
   requestUUID=$(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 $NF; }')
   request_status="in progress"
@@ -45,6 +45,6 @@ if false; then
   xcrun altool --notarization-info "$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 0.2.4 --install-location /Applications/AlphaTims.app --scripts scripts alphatims.pkg
+  pkgbuild --root dist/alphatims --identifier de.mpg.biochem.alphatims.app --version 0.2.5 --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 0.2.4</title>
+    <title>AlphaTims 0.2.5</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 "0.2.4"
+#define MyAppVersion "0.2.5"
 #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-0.2.4-py3-none-any.whl[plotting]"
+call pip install "../../dist/alphatims-0.2.5-py3-none-any.whl[plotting]"
 call pip install pyinstaller==4.2
 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-0.2.4-py3-none-any.whl[plotting]"
+pip install "../../dist/alphatims-0.2.5-py3-none-any.whl[plotting]"
 pip install pyinstaller==4.2
 # 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/misc/pyinstaller/alphatims_pyinstaller.py b/misc/pyinstaller/alphatims_pyinstaller.py
@@ -1,13 +1,7 @@
 if __name__ == "__main__":
     import alphatims.utils
-    log_file_name = alphatims.utils.set_logger(
-        log_file_name=alphatims.utils.INTERFACE_PARAMETERS["log_file"][
-            "default"
-        ]
-    )
-    threads = alphatims.utils.set_threads(
-        alphatims.utils.INTERFACE_PARAMETERS["threads"]["default"]
-    )
+    log_file_name = alphatims.utils.set_logger(log_file_name="")
+    threads = alphatims.utils.set_threads(-1)
     alphatims.utils.show_platform_info()
     alphatims.utils.show_python_info()
     alphatims.utils.check_github_version()