jupyter-analysis-tools 1.7.0__tar.gz → 1.7.2__tar.gz

{jupyter_analysis_tools-1.7.0 → jupyter_analysis_tools-1.7.2}/.copier-answers.yml

@@ -22,4 +22,4 @@ repo_main_branch: main
 repo_name: jupyter-analysis-tools
 repo_userorg: BAMresearch
 sphinx_theme: furo
-version: 1.7.0
+version: 1.7.2

{jupyter_analysis_tools-1.7.0 → jupyter_analysis_tools-1.7.2}/CHANGELOG.md

@@ -1,5 +1,21 @@
 # CHANGELOG
 
+## v1.7.2 (2026-01-30)
+
+### Bug fixes
+
+* **DataStore.__init__**: allow token-based auth, docs added ([`d64f92f`](https://github.com/BAMresearch/jupyter-analysis-tools/commit/d64f92fdcba4851497ff6782e4beee1109eb86bd))
+
+### Code style
+
+* **DataStore**: whitespace errors ([`f599040`](https://github.com/BAMresearch/jupyter-analysis-tools/commit/f5990401c80ec30a2748a5e2952ab806def207ac))
+
+## v1.7.1 (2025-12-11)
+
+### Bug fixes
+
+* **DataStore.createObject(**: attempt to create new project/collection only if object was not found; save it finally as well ([`95fa9e0`](https://github.com/BAMresearch/jupyter-analysis-tools/commit/95fa9e042a26b423936caac64d3e8b115790e888))
+
 ## v1.7.0 (2025-12-11)
 
 ### Code style

{jupyter_analysis_tools-1.7.0 → jupyter_analysis_tools-1.7.2}/PKG-INFO

@@ -1,6 +1,6 @@
 Metadata-Version: 2.4
 Name: jupyter-analysis-tools
-Version: 1.7.0
+Version: 1.7.2
 Summary: Yet another Python library with helpers and utilities for data analysis and processing.
 Author-email: Ingo Breßler <ingo.bressler@bam.de>, "Brian R. Pauw" <brian.pauw@bam.de>
 License-Expression: MIT
@@ -36,10 +36,10 @@ Requires-Dist: ipywidgets
 Requires-Dist: pybis
 Dynamic: license-file
 
-# Jupyter Analysis Tools (v1.7.0)
+# Jupyter Analysis Tools (v1.7.2)
 
 [![PyPI Package latest release](https://img.shields.io/pypi/v/jupyter-analysis-tools.svg)](https://pypi.org/project/jupyter-analysis-tools)
-[![Commits since latest release](https://img.shields.io/github/commits-since/BAMresearch/jupyter-analysis-tools/v1.7.0.svg)](https://github.com/BAMresearch/jupyter-analysis-tools/compare/v1.7.0...main)
+[![Commits since latest release](https://img.shields.io/github/commits-since/BAMresearch/jupyter-analysis-tools/v1.7.2.svg)](https://github.com/BAMresearch/jupyter-analysis-tools/compare/v1.7.2...main)
 [![License](https://img.shields.io/pypi/l/jupyter-analysis-tools.svg)](https://en.wikipedia.org/wiki/MIT_license)
 [![Supported versions](https://img.shields.io/pypi/pyversions/jupyter-analysis-tools.svg)](https://pypi.org/project/jupyter-analysis-tools)
 [![PyPI Wheel](https://img.shields.io/pypi/wheel/jupyter-analysis-tools.svg)](https://pypi.org/project/jupyter-analysis-tools#files)
@@ -98,6 +98,22 @@ are installed:
 
 # CHANGELOG
 
+## v1.7.2 (2026-01-30)
+
+### Bug fixes
+
+* **DataStore.__init__**: allow token-based auth, docs added ([`d64f92f`](https://github.com/BAMresearch/jupyter-analysis-tools/commit/d64f92fdcba4851497ff6782e4beee1109eb86bd))
+
+### Code style
+
+* **DataStore**: whitespace errors ([`f599040`](https://github.com/BAMresearch/jupyter-analysis-tools/commit/f5990401c80ec30a2748a5e2952ab806def207ac))
+
+## v1.7.1 (2025-12-11)
+
+### Bug fixes
+
+* **DataStore.createObject(**: attempt to create new project/collection only if object was not found; save it finally as well ([`95fa9e0`](https://github.com/BAMresearch/jupyter-analysis-tools/commit/95fa9e042a26b423936caac64d3e8b115790e888))
+
 ## v1.7.0 (2025-12-11)
 
 ### Code style

{jupyter_analysis_tools-1.7.0 → jupyter_analysis_tools-1.7.2}/README.md

@@ -1,7 +1,7 @@
-# Jupyter Analysis Tools (v1.7.0)
+# Jupyter Analysis Tools (v1.7.2)
 
 [![PyPI Package latest release](https://img.shields.io/pypi/v/jupyter-analysis-tools.svg)](https://pypi.org/project/jupyter-analysis-tools)
-[![Commits since latest release](https://img.shields.io/github/commits-since/BAMresearch/jupyter-analysis-tools/v1.7.0.svg)](https://github.com/BAMresearch/jupyter-analysis-tools/compare/v1.7.0...main)
+[![Commits since latest release](https://img.shields.io/github/commits-since/BAMresearch/jupyter-analysis-tools/v1.7.2.svg)](https://github.com/BAMresearch/jupyter-analysis-tools/compare/v1.7.2...main)
 [![License](https://img.shields.io/pypi/l/jupyter-analysis-tools.svg)](https://en.wikipedia.org/wiki/MIT_license)
 [![Supported versions](https://img.shields.io/pypi/pyversions/jupyter-analysis-tools.svg)](https://pypi.org/project/jupyter-analysis-tools)
 [![PyPI Wheel](https://img.shields.io/pypi/wheel/jupyter-analysis-tools.svg)](https://pypi.org/project/jupyter-analysis-tools#files)

{jupyter_analysis_tools-1.7.0 → jupyter_analysis_tools-1.7.2}/docs/conf.py

@@ -32,7 +32,7 @@ project = "Jupyter Analysis Tools"
 year = "2018-2025"
 author = "Ingo Breßler and Brian R. Pauw"
 copyright = "{0}, {1}".format(year, author)
-version = "1.7.0"
+version = "1.7.2"
 release = version
 commit_id = None
 try:

{jupyter_analysis_tools-1.7.0 → jupyter_analysis_tools-1.7.2}/src/jupyter_analysis_tools/__init__.py

@@ -1,7 +1,7 @@
 # -*- coding: utf-8 -*-
 # __init__.py
 
-__version__ = "1.7.0"
+__version__ = "1.7.2"
 
 from .binning import reBin
 from .git import checkRepo, isNBstripoutActivated, isNBstripoutInstalled, isRepo

{jupyter_analysis_tools-1.7.0 → jupyter_analysis_tools-1.7.2}/src/jupyter_analysis_tools/datastore.py

@@ -1,173 +1,201 @@
-# -*- coding: utf-8 -*-
-# datastore.py
-
-import filecmp
-import getpass
-import tempfile
-import warnings
-from pathlib import Path
-
-from pybis import Openbis
-
-
-class DataStore:
-    url = None
-    token = None
-    _availObj = None
-    _userspace = None
-
-    def __init__(self, url, username=None, tokenValidTo=None):
-        self.url = url
-        self.username = username
-        if self.username is None:
-            self.username = getpass.getuser()
-        print(f"Working as user '{self.username}'.")
-        # to generate PAT you need to login normally
-        self.ds = Openbis(url=self.url, verify_certificates=True)
-        # arg. *save_token* saves the openBIS token to ~/.pybis permanently
-        self.ds.login(
-            self.username,
-            getpass.getpass(prompt=f"Password for {self.username}: "),
-            save_token=False,
-        )
-        # create the PAT with the given name, don't store it
-        self.token = self.ds.get_or_create_personal_access_token(
-            "test-session", validTo=tokenValidTo
-        )
-
-    @property
-    def userspace(self):
-        uspace = self._userspace
-        if uspace is None:
-            allspaces = self.ds.get_spaces()
-            uspace = allspaces.df[
-                allspaces.df.code.str.endswith(self.username.upper())
-            ].code.values[0]
-            self._userspace = uspace
-        return uspace
-
-    @userspace.setter
-    def userspace(self, name):
-        name = name.upper()
-        if name in self.ds.get_spaces().df.code.values:
-            self._userspace = name
-
-    @staticmethod
-    def identifier(objects, code):
-        return objects[objects.code == code].identifier.tolist()[0]
-
-    def createProject(self, projectName, space, spacePrefix=None):
-        """Finds the requested project in the DataStore.
-        Matching project names can be limited to a given *spacePrefix*.
-        If the project is not found, a new project with the given code in the given space
-        is created."""
-        # get available projects, accessible by the current user
-        projectsAvail = self.ds.get_projects()
-        if spacePrefix:
-            projectsAvail = [prj for prj in projectsAvail if f"/{spacePrefix}_" in prj.identifier]
-        projects = [prj for prj in projectsAvail if prj.code == projectName]
-        assert len(projects) <= 1, f"Multiple projects found for '{projectName}'"
-        dsProject = None
-        if len(projects):  # get the existing object
-            dsProject = projects[0]
-        else:  # create it, if not found
-            print(f"Creating project '{projectName}'")
-            dsProject = self.ds.new_project(code=projectName, space=space)
-            dsProject.save()
-        assert dsProject
-        return dsProject
-
-    def createCollection(self, collName, projectObj, defaultObjType=None):
-        collections = self.ds.get_collections(project=projectObj)
-        dsColl = [coll for coll in collections if coll.code == collName.upper()]
-        if len(dsColl):
-            dsColl = dsColl[0]
-        else:  # create it, if not found
-            print(f"Creating collection '{collName}'")
-            dsColl = self.ds.new_collection(
-                code=collName, type="COLLECTION", project=projectObj, props={"$name": collName}
-            )
-            dsColl.save()
-        assert dsColl
-        # update properties (name, default view and object type) if not set)
-        props = dsColl.props.all()  # props as dict
-        propKey = "$name"
-        if propKey in props and props[propKey] is None:
-            props[propKey] = collName
-        propKey = "$default_collection_view"
-        if propKey in props.keys() and props[propKey] is None:
-            propVal = [
-                item
-                for item in self.ds.get_vocabulary(propKey + "s").get_terms().df.code
-                if "list" in item.lower()
-            ]
-            assert len(propVal)
-            props[propKey] = propVal[0]
-        if defaultObjType:
-            propKey = "$default_object_type"
-            if propKey in props.keys() and props[propKey] is None:
-                props[propKey] = defaultObjType
-        # print(f"Setting '{collName}' properties:\n  {props}")
-        dsColl.set_props(props)
-        dsColl.save()
-        return dsColl
-
-    def createObject(
-        self,
-        projectName: str,
-        collectionName: str = None,
-        space: str = None,
-        spacePrefix: str = None,
-        objType: str = None,
-        props: dict = None,
-    ):
-        dsProject = self.createProject(projectName, space, spacePrefix=spacePrefix)
-        dsColl = None
-        if collectionName is None:  # collectionName is required
-            return None
-        dsColl = self.createCollection(collectionName, dsProject, defaultObjType=objType)
-        obj = self.ds.get_objects(type=objType, where={"$name": props["$name"]}).objects
-        if len(obj):
-            obj = obj[0]
-            prefix = objType
-            msg = "'{}' exists already in {}! Updating ...".format(
-                obj.props["$name"], obj.project.identifier
-            )
-            warnings.warn_explicit(msg, UserWarning, prefix, 0)
-        else:  # does not exist yet
-            objName = f" '{props['$name']}'" if len(props.get("$name", "")) else ""
-            print(f"Creating new {objType}{objName} in {dsColl.identifier}")
-            obj = self.ds.new_object(type=objType, props=props, collection=dsColl)
-        obj.set_props(props)
-        return obj
-
-    def findObjects(self, *args, **kwargs):
-        return self.ds.get_objects(**kwargs)
-
-    def uploadDataset(self, obj, datasetType, fpaths=[]):
-        def _checkFile(localPath, remoteFiles):
-            remoteFile = [f for f in remoteFiles if f.name == localPath.name]
-            if not len(remoteFile):  # file exists in the dataset as well
-                return False
-            return filecmp.cmp(localPath, remoteFile[0], shallow=False)
-
-        if not len(fpaths):
-            return  # nothing to do
-        for dataset in obj.get_datasets(type=datasetType):
-            with tempfile.TemporaryDirectory() as tempdir:
-                dataset.download(destination=tempdir)
-                dsFiles = [f for f in Path(tempdir).rglob("*") if f.is_file()]
-                if len(fpaths) == len(dsFiles):
-                    if all([_checkFile(fpath, dsFiles) for fpath in fpaths]):
-                        print(
-                            f"All local files of {datasetType} match files in dataset, "
-                            "not updating."
-                        )
-                        continue  # skip deletion below
-            print(f"Dataset {datasetType} needs update, deleting existing dataset:")
-            dataset.delete("Needs update")
-        if not len(obj.get_datasets(type=datasetType)):  # didn't exist yet or all deleted
-            dataset = self.ds.new_dataset(
-                type=datasetType, collection=obj.collection, object=obj, files=fpaths
-            )
-            dataset.save()
+# -*- coding: utf-8 -*-
+# datastore.py
+
+import filecmp
+import getpass
+import tempfile
+import warnings
+from pathlib import Path
+
+from pybis import Openbis
+
+
+class DataStore:
+    url = None
+    token = None
+    _availObj = None
+    _userspace = None
+
+    def __init__(self, url, username=None, token=None, tokenValidTo=None):
+        """
+        Initialize the datastore connection and authenticate with openBIS.
+
+        Args:
+            url (str): The URL of the openBIS server.
+            username (str, optional): The username for authentication.
+                Defaults to the current system user if not provided.
+                It will as for the password interactively.
+            token (str, optional): A personal access token as retrieved by DataStore.token earlier
+                as alternative to username/password authentication.
+            tokenValidTo (str, optional): The expiration datetime for the new personal access token
+                when it is created using username/password authentication.
+
+        Raises:
+            Exception: If authentication fails or connection to the server cannot be established.
+
+        Note:
+            - If username is not provided, it defaults to the current system user.
+            - Password is prompted interactively via getpass.
+            - A personal access token named "test-session" is automatically created/retrieved.
+            - Token is not persisted to disk.
+        """
+        self.url = url
+        self.username = username
+        if self.username is None:
+            self.username = getpass.getuser()
+        print(f"Working as user '{self.username}'.")
+        # to generate PAT you need to login normally
+        self.ds = Openbis(url=self.url, verify_certificates=True)
+        # arg. *save_token* saves the openBIS token to ~/.pybis permanently
+        if token is not None:
+            if hasattr(token, "permId"):
+                token = token.permId
+            self.ds.set_token(token)
+        else:  # username/password login
+            self.ds.login(
+                self.username,
+                getpass.getpass(prompt=f"Password for {self.username}: "),
+                save_token=False,
+            )
+        # create the PAT with the given name, don't store it
+        self.token = self.ds.get_or_create_personal_access_token(
+            "test-session", validTo=tokenValidTo
+        )
+
+    @property
+    def userspace(self):
+        uspace = self._userspace
+        if uspace is None:
+            allspaces = self.ds.get_spaces()
+            uspace = allspaces.df[
+                allspaces.df.code.str.endswith(self.username.upper())
+            ].code.values[0]
+            self._userspace = uspace
+        return uspace
+
+    @userspace.setter
+    def userspace(self, name):
+        name = name.upper()
+        if name in self.ds.get_spaces().df.code.values:
+            self._userspace = name
+
+    @staticmethod
+    def identifier(objects, code):
+        return objects[objects.code == code].identifier.tolist()[0]
+
+    def createProject(self, projectName, space, spacePrefix=None):
+        """Finds the requested project in the DataStore.
+        Matching project names can be limited to a given *spacePrefix*.
+        If the project is not found, a new project with the given code in the given space
+        is created."""
+        # get available projects, accessible by the current user
+        projectsAvail = self.ds.get_projects()
+        if spacePrefix:
+            projectsAvail = [prj for prj in projectsAvail if f"/{spacePrefix}_" in prj.identifier]
+        projects = [prj for prj in projectsAvail if prj.code == projectName]
+        assert len(projects) <= 1, f"Multiple projects found for '{projectName}'"
+        dsProject = None
+        if len(projects):  # get the existing object
+            dsProject = projects[0]
+        else:  # create it, if not found
+            print(f"Creating project '{projectName}'")
+            dsProject = self.ds.new_project(code=projectName, space=space)
+            dsProject.save()
+        assert dsProject
+        return dsProject
+
+    def createCollection(self, collName, projectObj, defaultObjType=None):
+        collections = self.ds.get_collections(project=projectObj)
+        dsColl = [coll for coll in collections if coll.code == collName.upper()]
+        if len(dsColl):
+            dsColl = dsColl[0]
+        else:  # create it, if not found
+            print(f"Creating collection '{collName}'")
+            dsColl = self.ds.new_collection(
+                code=collName, type="COLLECTION", project=projectObj, props={"$name": collName}
+            )
+            dsColl.save()
+        assert dsColl
+        # update properties (name, default view and object type) if not set)
+        props = dsColl.props.all()  # props as dict
+        propKey = "$name"
+        if propKey in props and props[propKey] is None:
+            props[propKey] = collName
+        propKey = "$default_collection_view"
+        if propKey in props.keys() and props[propKey] is None:
+            propVal = [
+                item
+                for item in self.ds.get_vocabulary(propKey + "s").get_terms().df.code
+                if "list" in item.lower()
+            ]
+            assert len(propVal)
+            props[propKey] = propVal[0]
+        if defaultObjType:
+            propKey = "$default_object_type"
+            if propKey in props.keys() and props[propKey] is None:
+                props[propKey] = defaultObjType
+        # print(f"Setting '{collName}' properties:\n  {props}")
+        dsColl.set_props(props)
+        dsColl.save()
+        return dsColl
+
+    def createObject(
+        self,
+        projectName: str,
+        collectionName: str = None,
+        space: str = None,
+        spacePrefix: str = None,
+        objType: str = None,
+        props: dict = None,
+    ):
+        assert space and len(space), "space is required!"
+        assert projectName and len(projectName), "projectName is required!"
+        assert collectionName and len(collectionName), "collectionName is required!"
+        obj = self.ds.get_objects(type=objType, where={"$name": props["$name"]}).objects
+        if len(obj):
+            obj = obj[0]
+            prefix = objType
+            msg = "'{}' exists already in {}! Updating ...".format(
+                obj.props["$name"], obj.project.identifier
+            )
+            warnings.warn_explicit(msg, UserWarning, prefix, 0)
+        else:  # does not exist yet
+            dsProject = self.createProject(projectName, space, spacePrefix=spacePrefix)
+            dsColl = self.createCollection(collectionName, dsProject, defaultObjType=objType)
+            objName = f" '{props['$name']}'" if len(props.get("$name", "")) else ""
+            print(f"Creating new {objType}{objName} in {dsColl.identifier}")
+            obj = self.ds.new_object(type=objType, props=props, collection=dsColl)
+        obj.set_props(props)
+        obj.save()
+        return obj
+
+    def findObjects(self, *args, **kwargs):
+        return self.ds.get_objects(**kwargs)
+
+    def uploadDataset(self, obj, datasetType, fpaths=[]):
+        def _checkFile(localPath, remoteFiles):
+            remoteFile = [f for f in remoteFiles if f.name == localPath.name]
+            if not len(remoteFile):  # file exists in the dataset as well
+                return False
+            return filecmp.cmp(localPath, remoteFile[0], shallow=False)
+
+        if not len(fpaths):
+            return  # nothing to do
+        for dataset in obj.get_datasets(type=datasetType):
+            with tempfile.TemporaryDirectory() as tempdir:
+                dataset.download(destination=tempdir)
+                dsFiles = [f for f in Path(tempdir).rglob("*") if f.is_file()]
+                if len(fpaths) == len(dsFiles):
+                    if all([_checkFile(fpath, dsFiles) for fpath in fpaths]):
+                        print(
+                            f"All local files of {datasetType} match files in dataset, "
+                            "not updating."
+                        )
+                        continue  # skip deletion below
+            print(f"Dataset {datasetType} needs update, deleting existing dataset:")
+            dataset.delete("Needs update")
+        if not len(obj.get_datasets(type=datasetType)):  # didn't exist yet or all deleted
+            dataset = self.ds.new_dataset(
+                type=datasetType, collection=obj.collection, object=obj, files=fpaths
+            )
+            dataset.save()

{jupyter_analysis_tools-1.7.0 → jupyter_analysis_tools-1.7.2}/src/jupyter_analysis_tools.egg-info/PKG-INFO

@@ -1,6 +1,6 @@
 Metadata-Version: 2.4
 Name: jupyter-analysis-tools
-Version: 1.7.0
+Version: 1.7.2
 Summary: Yet another Python library with helpers and utilities for data analysis and processing.
 Author-email: Ingo Breßler <ingo.bressler@bam.de>, "Brian R. Pauw" <brian.pauw@bam.de>
 License-Expression: MIT
@@ -36,10 +36,10 @@ Requires-Dist: ipywidgets
 Requires-Dist: pybis
 Dynamic: license-file
 
-# Jupyter Analysis Tools (v1.7.0)
+# Jupyter Analysis Tools (v1.7.2)
 
 [![PyPI Package latest release](https://img.shields.io/pypi/v/jupyter-analysis-tools.svg)](https://pypi.org/project/jupyter-analysis-tools)
-[![Commits since latest release](https://img.shields.io/github/commits-since/BAMresearch/jupyter-analysis-tools/v1.7.0.svg)](https://github.com/BAMresearch/jupyter-analysis-tools/compare/v1.7.0...main)
+[![Commits since latest release](https://img.shields.io/github/commits-since/BAMresearch/jupyter-analysis-tools/v1.7.2.svg)](https://github.com/BAMresearch/jupyter-analysis-tools/compare/v1.7.2...main)
 [![License](https://img.shields.io/pypi/l/jupyter-analysis-tools.svg)](https://en.wikipedia.org/wiki/MIT_license)
 [![Supported versions](https://img.shields.io/pypi/pyversions/jupyter-analysis-tools.svg)](https://pypi.org/project/jupyter-analysis-tools)
 [![PyPI Wheel](https://img.shields.io/pypi/wheel/jupyter-analysis-tools.svg)](https://pypi.org/project/jupyter-analysis-tools#files)
@@ -98,6 +98,22 @@ are installed:
 
 # CHANGELOG
 
+## v1.7.2 (2026-01-30)
+
+### Bug fixes
+
+* **DataStore.__init__**: allow token-based auth, docs added ([`d64f92f`](https://github.com/BAMresearch/jupyter-analysis-tools/commit/d64f92fdcba4851497ff6782e4beee1109eb86bd))
+
+### Code style
+
+* **DataStore**: whitespace errors ([`f599040`](https://github.com/BAMresearch/jupyter-analysis-tools/commit/f5990401c80ec30a2748a5e2952ab806def207ac))
+
+## v1.7.1 (2025-12-11)
+
+### Bug fixes
+
+* **DataStore.createObject(**: attempt to create new project/collection only if object was not found; save it finally as well ([`95fa9e0`](https://github.com/BAMresearch/jupyter-analysis-tools/commit/95fa9e042a26b423936caac64d3e8b115790e888))
+
 ## v1.7.0 (2025-12-11)
 
 ### Code style