Merge pull request #183 from MannLabs/development

Development 1.2.5

.bumpversion.cfg

@@ -1,5 +1,5 @@
 [bumpversion]
-current_version = 1.2.4
+current_version = 1.2.5
 commit = True
 tag = False
 parse = (?P<major>\d+)\.(?P<minor>\d+)\.(?P<patch>\d+)(\-(?P<release>[a-z]+)(?P<build>\d+))?
@@ -28,6 +28,5 @@ serialize =
 [bumpversion:file:./release/one_click_windows_gui/create_installer_windows.sh]
 
 [bumpversion:file:./release/one_click_windows_gui/alphabase_innoinstaller.iss]
-
 search = {current_version}
 replace = {new_version}

.pre-commit-config.yaml

@@ -12,3 +12,5 @@ repos:
   hooks:
     - id: ruff-format
     - id: ruff
+
+exclude: .bumpversion.cfg

alphabase/__init__.py

@@ -2,7 +2,7 @@
 
 
 __project__ = "alphabase"
-__version__ = "1.2.4"
+__version__ = "1.2.5"
 __license__ = "Apache"
 __description__ = "An infrastructure Python package of the AlphaX ecosystem"
 __author__ = "Mann Labs"

alphabase/io/tempmmap.py

@@ -31,6 +31,71 @@ def _log_cleanup_info_once() -> None:
         is_cleanup_info_logged = True
 
 
+def _change_temp_dir_location(abs_path: str) -> str:
+    """
+    Check if the directory to which the temp arrays should be written exists, if so defines this as the new temp dir location. If not raise a value error.
+
+    Parameters
+    ----------
+    abs_path : str
+        The absolute path to the new temporary directory.
+
+    """
+
+    global TEMP_DIR_NAME
+
+    # ensure that the path exists
+    if os.path.exists(abs_path):
+        # ensure that the path points to a directory
+        if os.path.isdir(abs_path):
+            TEMP_DIR_NAME = abs_path
+        else:
+            raise ValueError(f"The path {abs_path} does not point to a directory.")
+    else:
+        raise ValueError(
+            f"The directory {abs_path} in which the file should be created does not exist."
+        )
+
+
+def _get_file_location(abs_file_path: str, overwrite=False) -> str:
+    """
+    Check if the path specified for the new temporary file is valid. If not raise a value error.
+
+    Valid file paths need to:
+    1. be contained in directories that exist
+    2. end in .hdf
+    3. not exist if overwrite is set to False
+
+    Parameters
+    ----------
+    abs_path : str
+        The absolute path to the new temporary file.
+
+    Returns
+    ------
+    str
+        The file path if it is valid.
+    """
+    # check overwrite status and existence of file
+    if not overwrite:
+        if os.path.exists(abs_file_path):
+            raise ValueError(
+                "The file already exists. Set overwrite to True to overwrite the file or choose a different name."
+            )
+
+    # ensure that the filename conforms to the naming convention
+    if not os.path.basename.endswith(".hdf"):
+        raise ValueError("The chosen file name needs to end with .hdf")
+
+    # ensure that the directory in which the file should be created exists
+    if os.path.isdir(os.path.commonpath(abs_file_path)):
+        return abs_file_path
+    else:
+        raise ValueError(
+            f"The directory {os.path.commonpath(abs_file_path)} in which the file should be created does not exist."
+        )
+
+
 def redefine_temp_location(path):
     """
     Redfine the location where the temp arrays are written to.
@@ -46,25 +111,27 @@ def redefine_temp_location(path):
 
     """
 
-    global _TEMP_DIR, _TEMP_DIR, TEMP_DIR_NAME
+    global _TEMP_DIR, TEMP_DIR_NAME
+
     logging.warning(
-        f"""Folder {TEMP_DIR_NAME} with temp mmap arrays is being deleted.All existing temp mmapp arrays will be unusable!"""
+        f"""Folder {TEMP_DIR_NAME} with temp mmap arrays is being deleted. All existing temp mmapp arrays will be unusable!"""
     )
 
     # cleaup old temporary directory
     shutil.rmtree(TEMP_DIR_NAME, ignore_errors=True)
-    del _TEMP_DIR
 
     # create new tempfile at desired location
-    _TEMP_DIR = tempfile.TemporaryDirectory(prefix=os.path.join(path, "temp_mmap"))
+    _TEMP_DIR = tempfile.TemporaryDirectory(prefix=os.path.join(path, "temp_mmap_"))
     TEMP_DIR_NAME = _TEMP_DIR.name
+
     logging.warning(
         f"""New temp folder location. Temp mmap arrays are written to {TEMP_DIR_NAME}. Cleanup of this folder is OS dependant, and might need to be triggered manually!"""
     )
+
     return TEMP_DIR_NAME
 
 
-def array(shape: tuple, dtype: np.dtype) -> np.ndarray:
+def array(shape: tuple, dtype: np.dtype, tmp_dir_abs_path: str = None) -> np.ndarray:
     """Create a writable temporary mmapped array.
 
     Parameters
@@ -73,14 +140,25 @@ def array(shape: tuple, dtype: np.dtype) -> np.ndarray:
         A tuple with the shape of the array.
     dtype : type
         The np.dtype of the array.
+    tmp_dir_abs_path : str, optional
+        If specified the memory mapped array will be created in this directory.
+        An absolute path is expected.
+        Defaults to None. If not specified the global TEMP_DIR_NAME location will be used.
 
     Returns
     -------
     type
         A writable temporary mmapped array.
     """
+    global TEMP_DIR_NAME
+
     _log_cleanup_info_once()
 
+    # redefine the temporary directory if a new location is given otherwise read from global variable
+    # this allows you to ensure that the correct temp directory location is used when working with multiple threads
+    if tmp_dir_abs_path is not None:
+        _change_temp_dir_location(tmp_dir_abs_path)
+
     temp_file_name = os.path.join(
         TEMP_DIR_NAME, f"temp_mmap_{np.random.randint(2**63)}.hdf"
     )
@@ -97,7 +175,13 @@ def array(shape: tuple, dtype: np.dtype) -> np.ndarray:
         ).reshape(shape)
 
 
-def create_empty_mmap(shape: tuple, dtype: np.dtype, path: str = None, overwrite=False):
+def create_empty_mmap(
+    shape: tuple,
+    dtype: np.dtype,
+    file_path: str = None,
+    overwrite: bool = False,
+    tmp_dir_abs_path: str = None,
+):
     """Initialize a new HDF5 file compatible with mmap. Returns the path to the initialized file.
     File can be mapped using the mmap_array_from_path function.
 
@@ -107,41 +191,37 @@ def create_empty_mmap(shape: tuple, dtype: np.dtype, path: str = None, overwrite
         A tuple with the shape of the array.
     dtype : type
         The np.dtype of the array.
-    path : str, optional
-        The path to the file that should be created.
+    file_path : str, optional
+        The absolute path to the file that should be created. This includes the file name.
         Defaults to None.
-        If None a random file name will be generated.
+        If None a random file name will be generated in the default tempdir location.
     overwrite : bool , optional
         If True the file will be overwritten if it already exists.
         Defaults to False.
+    tmp_dir_abs_path : str, optional
+        If specified the default tempdir location will be updated to this path. Defaults to None. An absolute path to a directory is expected.
 
     Returns
     -------
     str
         path to the newly created file.
     """
+    global TEMP_DIR_NAME
+
     _log_cleanup_info_once()
 
+    # redefine the temporary directory if a new location is given otherwise read from global variable
+    # this allows you to ensure that the correct temp directory location is used when working with multiple threads
+    if tmp_dir_abs_path is not None:
+        _change_temp_dir_location(tmp_dir_abs_path)
+
     # if path does not exist generate a random file name in the TEMP directory
-    if path is None:
+    if file_path is None:
         temp_file_name = os.path.join(
             TEMP_DIR_NAME, f"temp_mmap_{np.random.randint(2**63)}.hdf"
         )
     else:
-        # check that if overwrite is false the file does not already exist
-        if not overwrite:
-            if os.path.exists(path):
-                raise ValueError(
-                    "The file already exists. Set overwrite to True to overwrite the file or choose a different name."
-                )
-        if not os.path.basename.endswith(".hdf"):
-            raise ValueError("The chosen file name needs to end with .hdf")
-        if os.path.isdir(os.path.commonpath(path)):
-            temp_file_name = path
-        else:
-            raise ValueError(
-                "The directory in which the file should be created does not exist."
-            )
+        temp_file_name = _get_file_location(file_path, overwrite=False)
 
     with h5py.File(temp_file_name, "w") as hdf_file:
         array = hdf_file.create_dataset("array", shape=shape, dtype=dtype)
@@ -233,13 +313,15 @@ def clear() -> str:
     str
         The name of the new temporary folder.
     """
-    global _TEMP_DIR
-    global TEMP_DIR_NAME
+    global _TEMP_DIR, TEMP_DIR_NAME
+
     logging.warning(
         f"Folder {TEMP_DIR_NAME} with temp mmap arrays is being deleted. "
         "All existing temp mmapp arrays will be unusable!"
     )
+
     del _TEMP_DIR
+
     _TEMP_DIR = tempfile.TemporaryDirectory(prefix="temp_mmap_")
     TEMP_DIR_NAME = _TEMP_DIR.name
     return TEMP_DIR_NAME

alphabase/protein/fasta.py

@@ -46,7 +46,7 @@ def read_fasta_file(fasta_filename: str = ""):
         protein information,
         {protein_id:str, full_name:str, gene_name:str, description:str, sequence:str}
     """
-    with open(fasta_filename, "rt") as handle:
+    with open(fasta_filename, "rt", encoding="utf-8") as handle:
         iterator = SeqIO.parse(handle, "fasta")
         while iterator:
             try:

docs/conf.py

@@ -24,7 +24,7 @@
 copyright = "2022, Mann Labs, MPIB"
 author = "Mann Labs, MPIB"
 
-release = "1.2.4"
+release = "1.2.5"
 
 # -- General configuration ---------------------------------------------------
 

release/one_click_linux_gui/control

@@ -1,5 +1,5 @@
 Package: AlphaBase
-Version: 1.2.4
+Version: 1.2.5
 Architecture: all
 Maintainer: Mann Labs <[email protected]>
 Description: AlphaBase

release/one_click_linux_gui/create_installer_linux.sh

@@ -17,7 +17,7 @@ python setup.py sdist bdist_wheel
 # Setting up the local package
 cd release/one_click_linux_gui
 # Make sure you include the required extra packages and always use the stable or very-stable options!
-pip install "../../dist/alphabase-1.2.4-py3-none-any.whl[stable]"
+pip install "../../dist/alphabase-1.2.5-py3-none-any.whl[stable]"
 
 # Creating the stand-alone pyinstaller folder
 pip install pyinstaller

release/one_click_macos_gui/Info.plist

@@ -9,9 +9,9 @@
 	<key>CFBundleIconFile</key>
 	<string>alpha_logo.icns</string>
 	<key>CFBundleIdentifier</key>
-	<string>alphabase.1.2.4</string>
+	<string>alphabase.1.2.5</string>
 	<key>CFBundleShortVersionString</key>
-	<string>1.2.4</string>
+	<string>1.2.5</string>
 	<key>CFBundleInfoDictionaryVersion</key>
 	<string>6.0</string>
 	<key>CFBundleName</key>

release/one_click_macos_gui/create_installer_macos.sh

@@ -20,7 +20,7 @@ python setup.py sdist bdist_wheel
 
 # Setting up the local package
 cd release/one_click_macos_gui
-pip install "../../dist/alphabase-1.2.4-py3-none-any.whl[stable]"
+pip install "../../dist/alphabase-1.2.5-py3-none-any.whl[stable]"
 
 # Creating the stand-alone pyinstaller folder
 pip install pyinstaller
@@ -40,5 +40,5 @@ cp ../../LICENSE.txt Resources/LICENSE.txt
 cp ../logos/alpha_logo.png Resources/alpha_logo.png
 chmod 777 scripts/*
 
-pkgbuild --root dist/alphabase --identifier de.mpg.biochem.alphabase.app --version 1.2.4 --install-location /Applications/AlphaBase.app --scripts scripts AlphaBase.pkg
+pkgbuild --root dist/alphabase --identifier de.mpg.biochem.alphabase.app --version 1.2.5 --install-location /Applications/AlphaBase.app --scripts scripts AlphaBase.pkg
 productbuild --distribution distribution.xml --resources Resources --package-path AlphaBase.pkg dist/alphabase_gui_installer_macos.pkg

release/one_click_macos_gui/distribution.xml

@@ -1,6 +1,6 @@
 <?xml version="1.0" encoding="utf-8" standalone="no"?>
 <installer-script minSpecVersion="1.000000">
-    <title>AlphaBase 1.2.4</title>
+    <title>AlphaBase 1.2.5</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" />

release/one_click_windows_gui/alphabase_innoinstaller.iss

@@ -2,7 +2,7 @@
 ; SEE THE DOCUMENTATION FOR DETAILS ON CREATING INNO SETUP SCRIPT FILES!
 
 #define MyAppName "AlphaBase"
-#define MyAppVersion "1.2.4"
+#define MyAppVersion "1.2.5"
 #define MyAppPublisher "Max Planck Institute of Biochemistry and the University of Copenhagen, Mann Labs"
 #define MyAppURL "https://github.com/MannLabs/alphabase"
 #define MyAppExeName "alphabase_gui.exe"

release/one_click_windows_gui/create_installer_windows.sh

@@ -17,7 +17,7 @@ python setup.py sdist bdist_wheel
 # Setting up the local package
 cd release/one_click_windows_gui
 # Make sure you include the required extra packages and always use the stable or very-stable options!
-pip install "../../dist/alphabase-1.2.4-py3-none-any.whl[stable]"
+pip install "../../dist/alphabase-1.2.5-py3-none-any.whl[stable]"
 
 # Creating the stand-alone pyinstaller folder
 pip install pyinstaller