Changing name to package folder

.coveragerc

@@ -1,4 +1,4 @@
 [run]
 omit =
-    bam_data_store/_version.py
+    bam_masterdata/_version.py
     */__init__.py

.github/workflows/actions.yml

@@ -34,10 +34,10 @@ jobs:
         uv pip install -e '.[dev]'
     - name: mypy
       run: |
-        python -m mypy --ignore-missing-imports --follow-imports=silent --no-strict-optional --exclude dependencies bam_data_store tests
+        python -m mypy --ignore-missing-imports --follow-imports=silent --no-strict-optional --exclude dependencies bam_masterdata tests
     - name: Test with pytest
       run: |
-        python -m pytest -sv --ignore=bam_data_store/dependencies tests
+        python -m pytest -sv --ignore=bam_masterdata/dependencies tests
   build-and-install:
     runs-on: ubuntu-latest
     steps:
@@ -62,11 +62,11 @@ jobs:
         - uses: actions/checkout@v4
         - uses: chartboost/ruff-action@v1
           with:
-            args: "check . --exclude bam_data_store/dependencies"
+            args: "check . --exclude bam_masterdata/dependencies"
   ruff-formatting:
       runs-on: ubuntu-latest
       steps:
         - uses: actions/checkout@v4
         - uses: chartboost/ruff-action@v1
           with:
-            args: "format . --check --verbose --exclude bam_data_store/dependencies"
+            args: "format . --check --verbose --exclude bam_masterdata/dependencies"

.github/workflows/coveralls.yml

@@ -30,7 +30,7 @@ jobs:
         uv pip install coveralls
     - name: Build coverage file
       run: |
-        pytest --cov-config=.coveragerc --junitxml=pytest.xml --cov=bam_data_store tests | tee pytest-coverage.txt
+        pytest --cov-config=.coveragerc --junitxml=pytest.xml --cov=bam_masterdata tests | tee pytest-coverage.txt
     - name: Pytest coverage comment
       uses: MishaKav/pytest-coverage-comment@main
       with:

.gitignore

@@ -169,9 +169,9 @@ cython_debug/
 # Ruff
 .ruff_cache
 
-# static artifacts
-artifacts
-
 # pytest coverage
 pytest.xml
-pytest-coverage.txt
+pytest-coverage.txt
+
+# artifacts
+artifacts

.gitmodules

@@ -1,3 +1,3 @@
-[submodule "bam_data_store/dependencies/openbisschema"]
-	path = bam_data_store/dependencies/openbisschema
+[submodule "bam_masterdata/dependencies/openbisschema"]
+	path = bam_masterdata/dependencies/openbisschema
 	url = https://git.bam.de/bam-data-store/development/openbisschema.git

.vscode/settings.json

@@ -33,7 +33,7 @@
           "type": "debugpy",
           "request": "launch",
           "console": "integratedTerminal",
-          "program": "${workspaceFolder}/src/bam_data_store/app.py",  // path to your entry point Python module
+          "program": "${workspaceFolder}/src/bam_masterdata/app.py",  // path to your entry point Python module
       },
       {
           "name": "bds tests",
@@ -51,11 +51,11 @@
           ]
       },
       {
-        "name": "bds export-entities-to-json",
+        "name": "bds export-to-json",
         "type": "debugpy",
         "request": "launch",
         "cwd": "${workspaceFolder}",
-        "program": "${workspaceFolder}/.venv/bin/bam_data_store",
+        "program": "${workspaceFolder}/.venv/bin/bam_masterdata",
         "justMyCode": false,
         "args": ["export-entities-to-json"]
       },
@@ -64,7 +64,7 @@
         "type": "debugpy",
         "request": "launch",
         "cwd": "${workspaceFolder}",
-        "program": "${workspaceFolder}/.venv/bin/bam_data_store",
+        "program": "${workspaceFolder}/.venv/bin/bam_masterdata",
         "justMyCode": false,
         "args": ["export-entities-to-excel"]
       },

README.md

@@ -1,7 +1,6 @@
-# BAMDataStore
-
-This is the main repository of the BAM Data Store project. This is both a Python package and a web connecting the different resources for the Data Store.
+# BAM Masterdata
 
+The BAM Masterdata is a repository containing all the masterdata schema defining in BAM, as well as some utility functions to handle the masterdata.
 
 <!--
 ## Getting started
@@ -11,45 +10,51 @@ This is the main repository of the BAM Data Store project. This is both a Python
 ## Development
 
 If you want to develop locally this package, clone the project and enter in the workspace folder:
+
 ```sh
-git clone https://git.bam.de/bam-data-store/bam-data-store.git
-cd bam-data-store
+git clone https://git.bam.de/bam-data-store/bam-masterdata.git
+cd bam-masterdata
 ```
 
 Create a virtual environment (you can use Python>3.9) in your workspace:
+
 ```sh
 python3 -m venv .venv
 source .venv/bin/activate
 ```
 
 Run the following script:
+
 ```sh
 ./scripts/install_python_dependencies
 ```
 
-
 ### Run the tests
 
 You can locally run the tests by doing:
+
 ```sh
 python -m pytest -sv tests
 ```
 
 where the `-s` and `-v` options toggle the output verbosity.
 
 You can also generate a local coverage report:
+
 ```sh
 python -m pytest --cov=src tests
 ```
 
 ### Run auto-formatting and linting
 
 We use [Ruff](https://docs.astral.sh/ruff/) for formatting and linting the code following the rules specified in the `pyproject.toml`. You can run locally:
+
 ```sh
 ruff check .
 ```
 
 This will produce an output with the specific issues found. In order to auto-fix them, run:
+
 ```sh
 ruff format . --check
 ```
@@ -93,21 +98,25 @@ The settings configuration file `.vscode/settings.json` automatically applies th
 ### Documentation on Github pages
 
 To view the documentation locally, make sure to have installed the extra packages (this is part of the `scripts/install_python_dependencies.sh`, so if you ran this script before, you don't need to do it again now):
+
 ```sh
 uv pip install -e '[docu]'
 ```
 
 The first time, build the server:
+
 ```sh
 mkdocs build
 ```
 
 Run the documentation server:
+
 ```sh
 mkdocs serve
 ```
 
 The output looks like:
+
 ```sh
 INFO    -  Building documentation...
 INFO    -  Cleaning site directory
@@ -119,12 +128,12 @@ Simply click on `http://127.0.0.1:8000/`. The changes in the `md` files of the d
 
 ## Main contributors
 
-| Name | E-mail     | Role |
-|------|------------|--------|
-| Dr. Angela Ariza | [[email protected]](mailto:[email protected]) | Outreach and Training |
-| Caroline Demidova | [[email protected]](mailto:[email protected]) | Outreach and Training |
-| Daniel Kosztyla | [[email protected]](mailto:[email protected]) | IT |
-| Carlos Madariaga | [[email protected]](mailto:[email protected]) | Software Developer |
-| Kristina Meindl | [[email protected]](mailto:[email protected]) | Project Manager |
-| Dr. Jose M. Pizarro | [[email protected]](mailto:[email protected]) | Data Management |
-| Jörg Rädler | [[email protected]](mailto:[email protected]) | IT |
+| Name                | E-mail                                                       | Role                  |
+| ------------------- | ------------------------------------------------------------ | --------------------- |
+| Dr. Angela Ariza    | [[email protected]](mailto:[email protected])               | Outreach and Training |
+| Caroline Demidova   | [[email protected]](mailto:[email protected])     | Outreach and Training |
+| Daniel Kosztyla     | [[email protected]](mailto:[email protected])         | IT                    |
+| Carlos Madariaga    | [[email protected]](mailto:[email protected])       | Software Developer    |
+| Kristina Meindl     | [[email protected]](mailto:[email protected])         | Project Manager       |
+| Dr. Jose M. Pizarro | [[email protected]](mailto:[email protected]) | Data Management       |
+| Jörg Rädler       | [[email protected]](mailto:[email protected])             | IT                    |

bam_data_store/cli/cli.py → bam_masterdata/cli/cli.py

@@ -3,25 +3,25 @@
 import click
 from openpyxl import Workbook
 
-from bam_data_store.cli.entities_to_excel import entities_to_excel
-from bam_data_store.cli.entities_to_json import entities_to_json
-from bam_data_store.logger import logger
-from bam_data_store.utils import (
+from bam_masterdata.cli.entities_to_excel import entities_to_excel
+from bam_masterdata.cli.entities_to_json import entities_to_json
+from bam_masterdata.logger import logger
+from bam_masterdata.utils import (
     delete_and_create_dir,
     import_module,
     listdir_py_modules,
 )
 
 
-@click.group(help='Entry point to run `bam_data_store` CLI commands.')
+@click.group(help='Entry point to run `bam_masterdata` CLI commands.')
 def cli():
     pass
 
 
 @cli.command(help='Export entities to JSON files to the `./artifacts/` folder.')
 def export_entities_to_json():
     # Get the directories from the Python modules and the export directory for the static artifacts
-    datamodel_dir = os.path.join('.', 'bam_data_store', 'datamodel')
+    datamodel_dir = os.path.join('.', 'bam_masterdata', 'datamodel')
     export_dir = os.path.join('.', 'artifacts')
 
     # Delete and create the export directory
@@ -44,12 +44,12 @@ def export_entities_to_json():
 )
 def export_entities_to_excel():
     # Get the Python modules to process the datamodel
-    datamodel_dir = os.path.join('.', 'bam_data_store', 'datamodel')
+    datamodel_dir = os.path.join('.', 'bam_masterdata', 'datamodel')
     py_modules = listdir_py_modules(directory_path=datamodel_dir, logger=logger)
 
     # Load the definitions module classes
     definitions_module = import_module(
-        module_path='./bam_data_store/metadata/definitions.py'
+        module_path='./bam_masterdata/metadata/definitions.py'
     )
 
     # Process the modules and save the entities to the openBIS masterdata Excel file

bam_data_store/cli/entities_to_excel.py → bam_masterdata/cli/entities_to_excel.py

@@ -5,7 +5,7 @@
 if TYPE_CHECKING:
     from openpyxl.worksheet.worksheet import Worksheet
 
-from bam_data_store.utils import import_module
+from bam_masterdata.utils import import_module
 
 
 def entities_to_excel(

bam_data_store/cli/entities_to_json.py → bam_masterdata/cli/entities_to_json.py

@@ -8,7 +8,7 @@
 
 import click
 
-from bam_data_store.utils import delete_and_create_dir, import_module
+from bam_masterdata.utils import delete_and_create_dir, import_module
 
 
 def entities_to_json(

bam_data_store/datamodel/collection_types.py → bam_masterdata/datamodel/collection_types.py

@@ -1,8 +1,8 @@
-from bam_data_store.metadata.definitions import (
+from bam_masterdata.metadata.definitions import (
     CollectionTypeDef,
     PropertyTypeAssignment,
 )
-from bam_data_store.metadata.entities import CollectionType
+from bam_masterdata.metadata.entities import CollectionType
 
 
 class DefaultExperiment(CollectionType):

bam_data_store/datamodel/object_types.py → bam_masterdata/datamodel/object_types.py

@@ -1,5 +1,5 @@
-from bam_data_store.metadata.definitions import ObjectTypeDef, PropertyTypeAssignment
-from bam_data_store.metadata.entities import ObjectType
+from bam_masterdata.metadata.definitions import ObjectTypeDef, PropertyTypeAssignment
+from bam_masterdata.metadata.entities import ObjectType
 
 
 class Instrument(ObjectType):

bam_data_store/datamodel/property_types.py → bam_masterdata/datamodel/property_types.py

@@ -1,4 +1,4 @@
-from bam_data_store.metadata.definitions import PropertyTypeDef
+from bam_masterdata.metadata.definitions import PropertyTypeDef
 
 Name = PropertyTypeDef(
     version=1,

bam_data_store/datamodel/vocabulary_types.py → bam_masterdata/datamodel/vocabulary_types.py

@@ -1,8 +1,8 @@
-from bam_data_store.metadata.definitions import (
+from bam_masterdata.metadata.definitions import (
     VocabularyTerm,
     VocabularyTypeDef,
 )
-from bam_data_store.metadata.entities import VocabularyType
+from bam_masterdata.metadata.entities import VocabularyType
 
 
 class DocumentType(VocabularyType):

bam_data_store/metadata/entities.py → bam_masterdata/metadata/entities.py

@@ -3,7 +3,7 @@
 
 from pydantic import BaseModel, ConfigDict, Field, model_validator
 
-from bam_data_store.metadata.definitions import (
+from bam_masterdata.metadata.definitions import (
     CollectionTypeDef,
     ObjectTypeDef,
     PropertyTypeAssignment,

bam_data_store/utils/utils.py → bam_masterdata/utils/utils.py

@@ -2,7 +2,6 @@
 import importlib.util
 import os
 import shutil
-import sys
 from typing import TYPE_CHECKING, Any
 
 if TYPE_CHECKING:

mkdocs.yml

@@ -1,7 +1,7 @@
-site_name: BAM Data Store Wiki
-site_description: Documentation page for the BAM Data Store.
+site_name: BAM Masterdata
+site_description: Documentation page for the BAM Masterdata.
 site_author: BAM Data Store
-repo_url: https://github.com/BAMresearch/bam-data-store
+repo_url: https://github.com/BAMresearch/bam-masterdata
 nav:
   - Home: index.md
   - Tutorial:

pyproject.toml

@@ -13,7 +13,7 @@ classifiers = [
   "Programming Language :: Python :: 3.11",
   "Programming Language :: Python :: 3.12",
 ]
-name = "bam-data-store"
+name = "bam-masterdata"
 description = "The BAM Data Store utility tools and masterdata models wrapped in a Python package with a front-end web interface."
 dynamic = ["version"]
 readme = "README.md"
@@ -33,8 +33,8 @@ dependencies = [
 ]
 
 [project.urls]
-"Homepage" = "https://git.bam.de/bam-data-store/bam-data-store"
-"Bug Tracker" = "https://git.bam.de/bam-data-store/development/bam-data-store/issues"
+"Homepage" = "https://github.com/BAMresearch/bam-masterdata"
+"Bug Tracker" = "https://github.com/BAMresearch/bam-masterdata/issues"
 
 [project.optional-dependencies]
 dev = [
@@ -59,11 +59,11 @@ docu = [
 ]
 
 [project.scripts]
-bam_data_store = "bam_data_store.cli:cli"
+bam_masterdata = "bam_masterdata.cli:cli"
 
 [tool.ruff]
 # Exclude a variety of commonly ignored directories.
-include = ["bam_data_store/*.py", "tests/*.py"]
+include = ["bam_masterdata/*.py", "tests/*.py"]
 exclude = [
     ".bzr",
     ".direnv",
@@ -143,4 +143,4 @@ exclude = ["dependencies*"]
 namespaces = false
 
 [tool.setuptools_scm]
-write_to = "bam_data_store/_version.py"
+write_to = "bam_masterdata/_version.py"

scripts/install_python_dependencies.sh

@@ -16,7 +16,7 @@ echo "Installing main project dependencies..."
 uv pip install -e '.[dev,docu,jupy]'
 
 echo "Installing submodule dependencies..."
-SUBMODULE_PATH="bam_data_store/dependencies/openbisschema"
+SUBMODULE_PATH="bam_masterdata/dependencies/openbisschema"
 
 if [ -d "$SUBMODULE_PATH" ]; then
     pushd "$SUBMODULE_PATH" > /dev/null