Merge pull request #243 from MannLabs/develop

Develop

alphatims/__init__.py

@@ -2,7 +2,7 @@
 
 
 __project__ = "alphatims"
-__version__ = "1.0.5"
+__version__ = "1.0.6"
 __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/tempmmap.py

@@ -12,6 +12,9 @@
 import mmap
 import numpy as np
 
+# local
+import alphatims.utils
+
 
 def make_temp_dir(prefix: str = "temp_mmap_") -> tuple:
     """Make a temporary directory.
@@ -34,7 +37,7 @@ def make_temp_dir(prefix: str = "temp_mmap_") -> tuple:
 _TEMP_DIR, TEMP_DIR_NAME = make_temp_dir()
 ARRAYS = {}
 CLOSED = False
-ALLOW_NDARRAY_SUBCLASS = True
+ALLOW_NDARRAY_SUBCLASS = False
 
 logging.warning(
     f"WARNING: Temp mmap arrays are written to {TEMP_DIR_NAME}. "
@@ -162,6 +165,41 @@ def ones(shape: tuple, dtype: np.dtype) -> np.ndarray:
     return _array
 
 
+def arange(
+    start: int,
+    stop: int,
+    step: int = 1,
+    dtype: np.dtype = np.uint64
+) -> np.ndarray:
+    """Create a writable temporary mmapped array filled with as a range.
+
+    Parameters
+    ----------
+    start : int
+        The start of this range.
+    stop : int
+        The stop of this range.
+    step : int
+        The step of this range.
+    dtype : type
+        The np.dtype of the array.
+
+    Returns
+    -------
+    type
+        A writable temporary mmapped array filled as a range.
+    """
+    _array = empty((stop - start) // step, dtype)
+    fill_array(_array, start, stop, step)
+    return _array
+
+
+@alphatims.utils.njit(nogil=True)
+def fill_array(array, start, stop, step):
+    for index, value in enumerate(range(start, stop, step)):
+        array[index] = value
+
+
 def clone(array: np.ndarray) -> np.ndarray:
     """Create a writable temporary mmapped array copy.
 

alphatims/utils.py

@@ -162,7 +162,10 @@ def show_platform_info() -> None:
         f"cpu count     - {psutil.cpu_count()}"
         # f" ({100 - psutil.cpu_percent()}% unused)"
     )
-    logging.info(f"cpu frequency - {psutil.cpu_freq().current:.2f} Mhz")
+
+    # check if architecture is arm64 as psutil.cpu_freq() is not yet supported on apple silicon
+    if platform.machine() != 'arm64':
+        logging.info(f"cpu frequency - {psutil.cpu_freq().current:.2f} Mhz")
     logging.info(
         f"ram           - "
         f"{psutil.virtual_memory().available/1024**3:.1f}/"
@@ -424,7 +427,6 @@ def starfunc(iterable):
 def njit(_func=None, *args, **kwargs):
     """A wrapper for the numba.njit decorator.
 
-    The "cache" option is set to True by default.
     This can be overriden with kwargs.
 
     Parameters
@@ -442,11 +444,7 @@ def njit(_func=None, *args, **kwargs):
         A numba.njit decorated function.
     """
     import numba
-    if "cache" in kwargs:
-        cache = kwargs.pop("cache")
-    else:
-        cache = True
-    return numba.njit(_func, *args, cache=cache, **kwargs)
+    return numba.njit(_func, *args, **kwargs)
 
 
 def class_njit(
@@ -463,17 +461,28 @@ def parse_dict(dict_to_parse):
         result_dict = {}
         for key, value in dict_to_parse.items():
             if isinstance(value, pd.DataFrame):
-                key_module = types.ModuleType(f"{key}")
+                key_module = types.ModuleType(f"{value.__class__}_{id(value)}")
                 for column in value.columns:
                     key_module.__dict__[column] = np.array(
                         value[column].values,
                         copy=False
                     )
                 result_dict[key] = key_module
             else:
-                result_dict[key] = value
+                import numba.core.registry
+                if hasattr(value, "__dict__") and not isinstance(
+                    value,
+                    numba.core.registry.CPUDispatcher
+                ):
+                    key_module = types.ModuleType(f"{value.__class__}_{id(value)}")
+                    key_module.__dict__.update(parse_dict(value.__dict__))
+                    result_dict[key] = key_module
+                else:
+                    result_dict[key] = value
         return result_dict
     def wrapper(func):
+        import functools
+        @functools.wraps(func)
         def inner_func(self, *args, **kwargs):
             self_ = self
             self = types.ModuleType(f"{self.__class__}_{id(self)}")
@@ -490,14 +499,17 @@ def inner_func(self, *args, **kwargs):
             # ]
             tree.body[0].decorator_list = []
             tree.body[0].args.args = tree.body[0].args.args[1:]
-            tree.body[0].name = f"{func.__name__}_class_njit"
+            # tree.body[0].name = f"{func.__name__}_class_njit"
+            tree.body[0].name = f"{func.__name__}"
             src = ast.unparse(tree)
             env = dict(locals())
             env.update(globals())
             env["numba"] = numba
             exec(src, env, env)
-            src = f"self_.{func.__name__} = numba.njit(env['{func.__name__}_class_njit'])"
-#             src = f"self_.{func.__name__} = env['{func.__name__}_performance']"
+            # src = f"self_.{func.__name__} = numba.njit(env['{func.__name__}_class_njit'])"
+            # src = f"object.__setattr__(self_, '{func.__name__}', numba.njit(env['{func.__name__}_class_njit']))"
+            # src = f"self_.{func.__name__} = env['{func.__name__}_performance']"
+            src = f"object.__setattr__(self_, '{func.__name__}', numba.njit(env['{func.__name__}']))"
             exec(src)
             result = eval(f"self_.{func.__name__}(*args, **kwargs)")
             return result
@@ -513,7 +525,6 @@ def pjit(
     *,
     thread_count=None,
     include_progress_callback: bool = True,
-    cache: bool = True,
     **kwargs
 ):
     """A decorator that parallelizes the numba.njit decorator with threads.
@@ -543,9 +554,6 @@ def pjit(
         If False, no callback is added.
         See `set_progress_callback` for callback styles.
         Default is True.
-    cache : bool
-        See numba.njit decorator.
-        Default is True (in contrast to numba).
 
     Returns
     -------
@@ -558,13 +566,9 @@ def pjit(
     import numpy as np
 
     def parallel_compiled_func_inner(func):
-        if "cache" in kwargs:
-            cache = kwargs.pop("cache")
-        else:
-            cache = True
-        numba_func = numba.njit(nogil=True, cache=cache, **kwargs)(func)
+        numba_func = numba.njit(nogil=True, **kwargs)(func)
 
-        @numba.njit(nogil=True, cache=cache)
+        @numba.njit(nogil=True)
         def numba_func_parallel(
             iterable,
             thread_id,

misc/bumpversion.cfg

@@ -1,5 +1,5 @@
 [bumpversion]
-current_version = 1.0.5
+current_version = 1.0.6
 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: 1.0.5
+Version: 1.0.6
 Architecture: all
 Maintainer: Mann Labs <opensource@alphapept.com>
 Description: AlphaTims GUI

misc/one_click_linux/create_installer_linux.sh

@@ -12,8 +12,8 @@ rm -rf dist
 rm -rf build
 python setup.py sdist bdist_wheel
 cd misc/one_click_linux
-pip install "../../dist/alphatims-1.0.5-py3-none-any.whl[plotting-stable,stable,legacy-stable]"
-pip install pyinstaller==4.10
+pip install "../../dist/alphatims-1.0.6-py3-none-any.whl[plotting-stable,stable,legacy-stable]"
+pip install pyinstaller==5.6.2
 pyinstaller ../pyinstaller/alphatims.spec -y
 conda deactivate
 # mv dist/alphatims dist/AlphaTims

misc/one_click_macos/Info.plist

@@ -9,9 +9,9 @@
 	<key>CFBundleIconFile</key>
 	<string>alpha_logo.icns</string>
 	<key>CFBundleIdentifier</key>
-	<string>alphatims.1.0.5</string>
+	<string>alphatims.1.0.6</string>
 	<key>CFBundleShortVersionString</key>
-	<string>1.0.5</string>
+	<string>1.0.6</string>
 	<key>CFBundleInfoDictionaryVersion</key>
 	<string>6.0</string>
 	<key>CFBundleName</key>

misc/one_click_macos/create_installer_macos.sh

@@ -16,8 +16,8 @@ rm -rf dist
 rm -rf build
 python setup.py sdist bdist_wheel
 cd misc/one_click_macos
-pip install pyinstaller==4.10
-pip install "../../dist/alphatims-1.0.5-py3-none-any.whl[plotting-stable,stable,legacy-stable]"
+pip install pyinstaller==5.6.2
+pip install "../../dist/alphatims-1.0.6-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)" $f; done
   codesign --sign "Developer ID Application: Max-Planck-Gesellschaft zur Förderung der Wissenschaften e.V. (7QSY5527AQ)" dist/alphatims/Contents/MacOS/alphatims_gui --force --options=runtime --entitlements entitlements.xml
-  pkgbuild --root dist/alphatims --identifier de.mpg.biochem.alphatims.app --version 1.0.5 --install-location /Applications/AlphaTims.app --scripts scripts alphatims.pkg --sign "Developer ID Installer: Max-Planck-Gesellschaft zur Förderung der Wissenschaften e.V. (7QSY5527AQ)"
+  pkgbuild --root dist/alphatims --identifier de.mpg.biochem.alphatims.app --version 1.0.6 --install-location /Applications/AlphaTims.app --scripts scripts alphatims.pkg --sign "Developer ID Installer: Max-Planck-Gesellschaft zur Förderung der Wissenschaften e.V. (7QSY5527AQ)"
   productbuild --distribution distribution.xml --resources Resources --package-path alphatims.pkg dist/alphatims_gui_installer_macos.pkg --sign "Developer ID Installer: Max-Planck-Gesellschaft zur Förderung der Wissenschaften e.V. (7QSY5527AQ)"
   requestUUID=$(xcrun altool --notarize-app --primary-bundle-id "de.mpg.biochem.alphatims.app" --username "willems@biochem.mpg.de" --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 "willems@biochem.mpg.de" --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 1.0.5 --install-location /Applications/AlphaTims.app --scripts scripts alphatims.pkg
+  pkgbuild --root dist/alphatims --identifier de.mpg.biochem.alphatims.app --version 1.0.6 --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

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 1.0.5</title>
+    <title>AlphaTims 1.0.6</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" />

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 "1.0.5"
+#define MyAppVersion "1.0.6"
 #define MyAppPublisher "Max Planck Institute of Biochemistry, Mann department"
 #define MyAppURL "https://github.com/MannLabs/alphatims"
 #define MyAppExeName "alphatims_gui.exe"

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-1.0.5-py3-none-any.whl[plotting-stable,stable,legacy-stable]"
+call pip install "../../dist/alphatims-1.0.6-py3-none-any.whl[plotting-stable,stable,legacy-stable]"
 call pip install pyinstaller==4.10
 call pyinstaller ../pyinstaller/alphatims.spec -y
 call conda deactivate

misc/one_click_windows/create_installer_windows.sh

@@ -7,8 +7,8 @@ rm -rf dist
 rm -rf build
 python setup.py sdist bdist_wheel
 cd misc/one_click_windows
-pip install "../../dist/alphatims-1.0.5-py3-none-any.whl[plotting-stable,stable,legacy-stable]"
-pip install pyinstaller==4.10
+pip install "../../dist/alphatims-1.0.6-py3-none-any.whl[plotting-stable,stable,legacy-stable]"
+pip install pyinstaller==5.6.2
 # TODO https://stackoverflow.com/questions/54175042/python-3-7-anaconda-environment-import-ssl-dll-load-fail-error/60405693#60405693
 pyinstaller ../pyinstaller/alphatims.spec -y
 conda deactivate

requirements/requirements_development.txt

@@ -1,6 +1,6 @@
 jupyter==1.0.0
 jupyter_contrib_nbextensions==0.5.1
-pyinstaller==4.10
+pyinstaller==5.6.2
 autodocsumm==0.2.7
 sphinx-rtd-theme==0.5.2
 plotly==4.12.0