junifer 0.0.8.dev184__tar.gz → 0.0.8.dev193__tar.gz

{junifer-0.0.8.dev184 → junifer-0.0.8.dev193}/PKG-INFO

@@ -1,6 +1,6 @@
 Metadata-Version: 2.4
 Name: junifer
-Version: 0.0.8.dev184
+Version: 0.0.8.dev193
 Summary: JUelich NeuroImaging FEature extractoR
 Author-email: Fede Raimondo <f.raimondo@fz-juelich.de>, Synchon Mandal <s.mandal@fz-juelich.de>
 Maintainer-email: Fede Raimondo <f.raimondo@fz-juelich.de>, Synchon Mandal <s.mandal@fz-juelich.de>

junifer-0.0.8.dev193/docs/changes/newsfragments/502.bugfix

@@ -0,0 +1 @@
+Fix type issues and update model configs for :class:`.BaseDataGrabber`, :class:`.BasePreprocessor`, :class:`.BaseMarker` and :class:`.BaseStorage` by `Synchon Mandal`_

junifer-0.0.8.dev193/docs/changes/newsfragments/503.enh

@@ -0,0 +1 @@
+Revert ``pre_run`` and ``pre_collect`` parameters for queue context adapters by `Synchon Mandal`_

{junifer-0.0.8.dev184 → junifer-0.0.8.dev193}/junifer/_version.py

@@ -18,7 +18,7 @@ version_tuple: tuple[int | str, ...]
 commit_id: str | None
 __commit_id__: str | None
 
-__version__ = version = '0.0.8.dev184'
-__version_tuple__ = version_tuple = (0, 0, 8, 'dev184')
+__version__ = version = '0.0.8.dev193'
+__version_tuple__ = version_tuple = (0, 0, 8, 'dev193')
 
-__commit_id__ = commit_id = 'g32666e1bf'
+__commit_id__ = commit_id = 'g8d610dbb9'

{junifer-0.0.8.dev184 → junifer-0.0.8.dev193}/junifer/api/queue_context/gnu_parallel_local_adapter.py

@@ -35,9 +35,9 @@ class GnuParallelLocalAdapter(QueueContextAdapter):
         The path to the YAML config file.
     elements : ``Elements``
         Element(s) to process. Will be used to index the DataGrabber.
-    pre_run_cmds : str or None, optional
+    pre_run : str or None, optional
         Extra shell commands to source before the run (default None).
-    pre_collect_cmds : str or None, optional
+    pre_collect : str or None, optional
         Extra shell commands to source before the collect (default None).
     env : :class:`.QueueContextEnv` or None, optional
         The environment configuration. If None, will run without a
@@ -63,8 +63,8 @@ class GnuParallelLocalAdapter(QueueContextAdapter):
     job_dir: Path
     yaml_config_path: Path
     elements: Elements
-    pre_run_cmds: str | None = None
-    pre_collect_cmds: str | None = None
+    pre_run: str | None = None
+    pre_collect: str | None = None
     env: QueueContextEnv | None = None
     verbose: str = "info"
     verbose_datalad: str | None = None
@@ -105,7 +105,7 @@ class GnuParallelLocalAdapter(QueueContextAdapter):
 
         return "\n".join(elements_to_run)
 
-    def pre_run(self) -> str:
+    def pre_run_cmds(self) -> str:
         """Return pre-run commands."""
         fixed = (
             f"#!/usr/bin/env {self.env['shell']}\n\n"
@@ -113,10 +113,10 @@ class GnuParallelLocalAdapter(QueueContextAdapter):
             "# Force datalad to run in non-interactive mode\n"
             "DATALAD_UI_INTERACTIVE=false\n"
         )
-        var = self.pre_run_cmds or ""
+        var = self.pre_run or ""
         return fixed + "\n" + var
 
-    def run(self) -> str:
+    def run_cmds(self) -> str:
         """Return run commands."""
         verbose_args = f"--verbose {self.verbose}"
         if self.verbose_datalad:
@@ -141,16 +141,16 @@ class GnuParallelLocalAdapter(QueueContextAdapter):
             f"--element"
         )
 
-    def pre_collect(self) -> str:
+    def pre_collect_cmds(self) -> str:
         """Return pre-collect commands."""
         fixed = (
             f"#!/usr/bin/env {self.env['shell']}\n\n"
             "# This script is auto-generated by junifer.\n"
         )
-        var = self.pre_collect_cmds or ""
+        var = self.pre_collect or ""
         return fixed + "\n" + var
 
-    def collect(self) -> str:
+    def collect_cmds(self) -> str:
         """Return collect commands."""
         verbose_args = f"--verbose {self.verbose}"
         if self.verbose_datalad:
@@ -196,14 +196,14 @@ class GnuParallelLocalAdapter(QueueContextAdapter):
             f"Writing {self._pre_run_path.name} to {self.job_dir.resolve()!s}"
         )
         self._pre_run_path.touch()
-        self._pre_run_path.write_text(textwrap.dedent(self.pre_run()))
+        self._pre_run_path.write_text(textwrap.dedent(self.pre_run_cmds()))
         make_executable(self._pre_run_path)
         # Create run
         logger.info(
             f"Writing {self._run_path.name} to {self.job_dir.resolve()!s}"
         )
         self._run_path.touch()
-        self._run_path.write_text(textwrap.dedent(self.run()))
+        self._run_path.write_text(textwrap.dedent(self.run_cmds()))
         make_executable(self._run_path)
         # Create pre collect
         logger.info(
@@ -211,14 +211,16 @@ class GnuParallelLocalAdapter(QueueContextAdapter):
             f"{self.job_dir.resolve()!s}"
         )
         self._pre_collect_path.touch()
-        self._pre_collect_path.write_text(textwrap.dedent(self.pre_collect()))
+        self._pre_collect_path.write_text(
+            textwrap.dedent(self.pre_collect_cmds())
+        )
         make_executable(self._pre_collect_path)
         # Create collect
         logger.info(
             f"Writing {self._collect_path.name} to {self.job_dir.resolve()!s}"
         )
         self._collect_path.touch()
-        self._collect_path.write_text(textwrap.dedent(self.collect()))
+        self._collect_path.write_text(textwrap.dedent(self.collect_cmds()))
         make_executable(self._collect_path)
         # Submit if required
         run_cmd = f"sh {self._run_path.resolve()!s}"

{junifer-0.0.8.dev184 → junifer-0.0.8.dev193}/junifer/api/queue_context/htcondor_adapter.py

@@ -52,9 +52,9 @@ class HTCondorAdapter(QueueContextAdapter):
         The path to the YAML config file.
     elements : ``Elements``
         Element(s) to process. Will be used to index the DataGrabber.
-    pre_run_cmds : str or None, optional
+    pre_run : str or None, optional
         Extra shell commands to source before the run (default None).
-    pre_collect_cmds : str or None, optional
+    pre_collect : str or None, optional
         Extra shell commands to source before the collect (default None).
     env : :class:`.QueueContextEnv` or None, optional
         The environment configuration. If None, will run without a
@@ -91,8 +91,8 @@ class HTCondorAdapter(QueueContextAdapter):
     job_dir: Path
     yaml_config_path: Path
     elements: Elements
-    pre_run_cmds: str | None = None
-    pre_collect_cmds: str | None = None
+    pre_run: str | None = None
+    pre_collect: str | None = None
     env: QueueContextEnv | None = None
     verbose: str = "info"
     verbose_datalad: str | None = None
@@ -127,7 +127,7 @@ class HTCondorAdapter(QueueContextAdapter):
         )
         self._dag_path = self.job_dir / f"{self.job_name}.dag"
 
-    def pre_run(self) -> str:
+    def pre_run_cmds(self) -> str:
         """Return pre-run commands."""
         fixed = (
             f"#!/usr/bin/env {self.env['shell']}\n\n"
@@ -135,10 +135,10 @@ class HTCondorAdapter(QueueContextAdapter):
             "# Force datalad to run in non-interactive mode\n"
             "DATALAD_UI_INTERACTIVE=false\n"
         )
-        var = self.pre_run_cmds or ""
+        var = self.pre_run or ""
         return fixed + "\n" + var
 
-    def run(self) -> str:
+    def run_cmds(self) -> str:
         """Return run commands."""
         verbose_args = f"--verbose {self.verbose} "
         if self.verbose_datalad is not None:
@@ -176,19 +176,19 @@ class HTCondorAdapter(QueueContextAdapter):
         var = self.extra_preamble or ""
         return fixed + "\n" + var + "\n" + "queue"
 
-    def pre_collect(self) -> str:
+    def pre_collect_cmds(self) -> str:
         """Return pre-collect commands."""
         fixed = (
             f"#!/usr/bin/env {self.env['shell']}\n\n"
             "# This script is auto-generated by junifer.\n"
         )
-        var = self.pre_collect_cmds or ""
+        var = self.pre_collect or ""
         # Add commands if collect="yes"
         if self.collect_task == "yes":
             var += 'if [ "${1}" == "4" ]; then\n    exit 1\nfi\n'
         return fixed + "\n" + var
 
-    def collect(self) -> str:
+    def collect_cmds(self) -> str:
         """Return collect commands."""
         verbose_args = f"--verbose {self.verbose} "
         if self.verbose_datalad is not None:
@@ -222,7 +222,7 @@ class HTCondorAdapter(QueueContextAdapter):
         var = self.extra_preamble or ""
         return fixed + "\n" + var + "\n" + "queue"
 
-    def dag(self) -> str:
+    def dag_cmds(self) -> str:
         """Return HTCondor DAG commands."""
         fixed = ""
         for idx, element in enumerate(self.elements):
@@ -277,7 +277,7 @@ class HTCondorAdapter(QueueContextAdapter):
             f"Writing {self._pre_run_path.name} to {self.job_dir.resolve()!s}"
         )
         self._pre_run_path.touch()
-        self._pre_run_path.write_text(textwrap.dedent(self.pre_run()))
+        self._pre_run_path.write_text(textwrap.dedent(self.pre_run_cmds()))
         make_executable(self._pre_run_path)
         # Create run
         logger.debug(
@@ -285,14 +285,16 @@ class HTCondorAdapter(QueueContextAdapter):
             f"{self.job_dir.resolve()!s}"
         )
         self._submit_run_path.touch()
-        self._submit_run_path.write_text(textwrap.dedent(self.run()))
+        self._submit_run_path.write_text(textwrap.dedent(self.run_cmds()))
         # Create pre collect
         logger.info(
             f"Writing {self._pre_collect_path.name} to "
             f"{self.job_dir.resolve()!s}"
         )
         self._pre_collect_path.touch()
-        self._pre_collect_path.write_text(textwrap.dedent(self.pre_collect()))
+        self._pre_collect_path.write_text(
+            textwrap.dedent(self.pre_collect_cmds())
+        )
         make_executable(self._pre_collect_path)
         # Create collect
         logger.debug(
@@ -300,13 +302,15 @@ class HTCondorAdapter(QueueContextAdapter):
             f"{self.job_dir.resolve()!s}"
         )
         self._submit_collect_path.touch()
-        self._submit_collect_path.write_text(textwrap.dedent(self.collect()))
+        self._submit_collect_path.write_text(
+            textwrap.dedent(self.collect_cmds())
+        )
         # Create DAG
         logger.debug(
             f"Writing {self._dag_path.name} to {self.job_dir.resolve()!s}"
         )
         self._dag_path.touch()
-        self._dag_path.write_text(textwrap.dedent(self.dag()))
+        self._dag_path.write_text(textwrap.dedent(self.dag_cmds()))
         # Submit if required
         condor_submit_dag_cmd = [
             "condor_submit_dag",

{junifer-0.0.8.dev184 → junifer-0.0.8.dev193}/junifer/api/queue_context/queue_context_adapter.py

@@ -64,11 +64,11 @@ class QueueContextAdapter(BaseModel, ABC):
 
     model_config = ConfigDict(
         use_enum_values=True,
-        extra="allow",
+        extra="forbid",
     )
 
     @abstractmethod
-    def pre_run(self) -> str:
+    def pre_run_cmds(self) -> str:
         """Return pre-run commands."""
         raise_error(
             msg="Concrete classes need to implement pre_run()",
@@ -76,7 +76,7 @@ class QueueContextAdapter(BaseModel, ABC):
         )
 
     @abstractmethod
-    def run(self) -> str:
+    def run_cmds(self) -> str:
         """Return run commands."""
         raise_error(
             msg="Concrete classes need to implement run()",
@@ -84,7 +84,7 @@ class QueueContextAdapter(BaseModel, ABC):
         )
 
     @abstractmethod
-    def pre_collect(self) -> str:
+    def pre_collect_cmds(self) -> str:
         """Return pre-collect commands."""
         raise_error(
             msg="Concrete classes need to implement pre_collect()",
@@ -92,7 +92,7 @@ class QueueContextAdapter(BaseModel, ABC):
         )
 
     @abstractmethod
-    def collect(self) -> str:
+    def collect_cmds(self) -> str:
         """Return collect commands."""
         raise_error(
             msg="Concrete classes need to implement collect()",

{junifer-0.0.8.dev184 → junifer-0.0.8.dev193}/junifer/api/queue_context/tests/test_gnu_parallel_local_adapter.py

@@ -73,10 +73,10 @@ def test_GnuParallelLocalAdapter_pre_run(
         yaml_config_path=Path("."),
         elements=["sub01"],
         env={"kind": "conda", "name": "junifer", "shell": shell},
-        pre_run_cmds=pre_run,
+        pre_run=pre_run,
     )
-    assert shell in adapter.pre_run()
-    assert expected_text in adapter.pre_run()
+    assert shell in adapter.pre_run_cmds()
+    assert expected_text in adapter.pre_run_cmds()
 
 
 @pytest.mark.parametrize(
@@ -111,10 +111,10 @@ def test_GnuParallelLocalAdapter_pre_collect(
         yaml_config_path=Path("."),
         elements=["sub01"],
         env={"kind": "venv", "name": "junifer", "shell": shell},
-        pre_collect_cmds=pre_collect,
+        pre_collect=pre_collect,
     )
-    assert shell in adapter.pre_collect()
-    assert expected_text in adapter.pre_collect()
+    assert shell in adapter.pre_collect_cmds()
+    assert expected_text in adapter.pre_collect_cmds()
 
 
 def test_GnuParallelLocalAdapter_run() -> None:
@@ -125,7 +125,7 @@ def test_GnuParallelLocalAdapter_run() -> None:
         yaml_config_path=Path("."),
         elements=["sub01"],
     )
-    assert "run" in adapter.run()
+    assert "run" in adapter.run_cmds()
 
 
 def test_GnuParallelLocalAdapter_collect() -> None:
@@ -136,7 +136,7 @@ def test_GnuParallelLocalAdapter_collect() -> None:
         yaml_config_path=Path("."),
         elements=["sub01"],
     )
-    assert "collect" in adapter.collect()
+    assert "collect" in adapter.collect_cmds()
 
 
 @pytest.mark.parametrize(

{junifer-0.0.8.dev184 → junifer-0.0.8.dev193}/junifer/api/queue_context/tests/test_htcondor_adapter.py

@@ -43,10 +43,10 @@ def test_HTCondorAdapter_pre_run(
         yaml_config_path=Path("."),
         elements=["sub01"],
         env={"kind": "conda", "name": "junifer", "shell": shell},
-        pre_run_cmds=pre_run,
+        pre_run=pre_run,
     )
-    assert shell in adapter.pre_run()
-    assert expected_text in adapter.pre_run()
+    assert shell in adapter.pre_run_cmds()
+    assert expected_text in adapter.pre_run_cmds()
 
 
 @pytest.mark.parametrize(
@@ -88,11 +88,11 @@ def test_HTCondorAdapter_pre_collect(
         yaml_config_path=Path("."),
         elements=["sub01"],
         env={"kind": "venv", "name": "junifer", "shell": shell},
-        pre_collect_cmds=pre_collect,
+        pre_collect=pre_collect,
         collect_task=collect,
     )
-    assert shell in adapter.pre_collect()
-    assert expected_text in adapter.pre_collect()
+    assert shell in adapter.pre_collect_cmds()
+    assert expected_text in adapter.pre_collect_cmds()
 
 
 @pytest.mark.parametrize(
@@ -122,8 +122,8 @@ def test_HTCondorAdapter_run_collect(
         elements=["sub01"],
         extra_preamble=extra_preamble,
     )
-    assert expected_text in adapter.run()
-    assert expected_text in adapter.collect()
+    assert expected_text in adapter.run_cmds()
+    assert expected_text in adapter.collect_cmds()
 
 
 @pytest.mark.parametrize(
@@ -165,7 +165,7 @@ def test_HTCondor_dag(
         elements=elements,
         collect_task=collect,
     )
-    assert expected_text in adapter.dag()
+    assert expected_text in adapter.dag_cmds()
 
 
 @pytest.mark.parametrize(

{junifer-0.0.8.dev184 → junifer-0.0.8.dev193}/junifer/datagrabber/base.py

@@ -13,7 +13,7 @@ from typing import Annotated, Any
 
 import structlog
 from aenum import Enum as AEnum
-from pydantic import BaseModel, BeforeValidator, ConfigDict, Field
+from pydantic import BaseModel, BeforeValidator, ConfigDict
 
 from ..pipeline import UpdateMetaMixin
 from ..typing import Element, Elements
@@ -58,11 +58,10 @@ class BaseDataGrabber(BaseModel, ABC, UpdateMetaMixin):
 
     """
 
-    model_config = ConfigDict(use_enum_values=True)
+    model_config = ConfigDict(extra="forbid", use_enum_values=True)
 
     types: Annotated[
         DataType | list[DataType],
-        Field(frozen=True),
         BeforeValidator(ensure_list),
     ]
     datadir: Path

junifer-0.0.8.dev193/junifer/external/BrainPrint/.codecov.yml

@@ -0,0 +1,2 @@
+github_checks:
+  annotations: false

junifer-0.0.8.dev193/junifer/external/BrainPrint/.codespellignore

@@ -0,0 +1,2 @@
+coo
+daty

junifer-0.0.8.dev193/junifer/external/BrainPrint/.github/ISSUE_TEMPLATE/bug-report.md

@@ -0,0 +1,45 @@
+---
+name: Bug Report
+about: Create a bug report to help us improve BrainPrint
+title: ''
+labels: bug
+assignees: ''
+
+---
+
+## Description
+<!-- A clear and concise description of the observed bug and/or error -->
+....
+
+## Steps to Reproduce
+<!-- 
+Steps to reproduce the observed behaviour, in as much detail as possible:
+1. Go to '...'
+2. Checkout version '...'
+3. Run '....'
+4. See error
+-->
+
+<!-- If possible, provide error messages, stack traces, and any snippets useful in describing the bug here -->
+...
+
+## Expected Behavior
+<!-- A clear and concise description of what you expected to happen. -->
+...
+
+## Screenshots
+<!-- If applicable and desired, add screenshots to help illustrate your problem. -->
+...
+
+## Environment
+ - BrainPrint Version: ...
+ - OS: ...
+ - CPU: ...
+
+<!-- Add any other relevant information on the environment here -->
+
+<!-- If possible, include a snapshot of the python software package versions you have (for e.g., using pip freeze or conda list) here -->
+
+## Additional Context
+<!-- Add any other context and comments about the problem here. -->
+...

junifer-0.0.8.dev193/junifer/external/BrainPrint/.github/ISSUE_TEMPLATE/documentation.md

@@ -0,0 +1,12 @@
+---
+name: Documentation
+about: Report an issue or make a suggestion related to BrainPrint documentation
+title: ''
+labels: documentation
+assignees: ''
+
+---
+
+## Documentation
+<!-- A clear and concise description of an issue you observed in the documentation, or a suggestion you wish to make. -->
+...

junifer-0.0.8.dev193/junifer/external/BrainPrint/.github/ISSUE_TEMPLATE/feature-request.md

@@ -0,0 +1,24 @@
+---
+name: Feature Request
+about: Submit a proposal/request for a new BrainPrint feature
+title: ''
+labels: enhancement
+assignees: ''
+
+---
+
+## Feature Description
+<!-- A clear and concise description of the feature you would like to propose -->
+...
+
+## Motivation
+<!-- A clear and concise description of the problem that the proposed feature would address. For e.g., I'm always frustrated when [...]. If this is related to a specific issue, refer to it here -->
+...
+
+## Alternatives
+<!-- A clear and concise description of any alternative solutions or features you've considered, if any. -->
+...
+
+## Additional Context
+<!-- Add any other context or screenshots about the feature request here. -->
+...

junifer-0.0.8.dev193/junifer/external/BrainPrint/.github/ISSUE_TEMPLATE/questions-help-support.md

@@ -0,0 +1,28 @@
+---
+name: Questions/Help/Support
+about: Submit a request for support or a question
+title: ''
+labels: question
+assignees: ''
+
+---
+
+## Question/Support Request
+<!-- A clear and concise description of a question you may have or a problem for which you would like to request support  -->
+...
+
+## Screenshots
+<!-- If possible, add screenshots to help illustrate your problem. -->
+...
+
+<!-- If applicable, provide error messages, stack traces, and any snippets useful in describing your problem here -->
+
+## Environment
+ - BrainPrint Version: ...
+ - OS: ...
+ - CPU: ...
+
+<!-- Add any other relevant information on the environment here -->
+
+<!-- If possible, include a snapshot of the python software package versions you have (for e.g., using pip freeze or conda list) here -->
+

junifer-0.0.8.dev193/junifer/external/BrainPrint/.github/dependabot.yml

@@ -0,0 +1,6 @@
+version: 2
+updates:
+  - package-ecosystem: "github-actions"
+    directory: "/"
+    schedule:
+      interval: "weekly"

junifer-0.0.8.dev193/junifer/external/BrainPrint/.github/workflows/build.yml

@@ -0,0 +1,53 @@
+name: build
+concurrency:
+  group: ${{ github.workflow }}-${{ github.event.number }}-${{ github.event.ref }}
+  cancel-in-progress: true
+on:
+  pull_request:
+  push:
+    branches: [main]
+  workflow_dispatch:
+
+jobs:
+  build:
+    timeout-minutes: 10
+    strategy:
+      fail-fast: false
+      matrix:
+        os: [ubuntu, macos, windows]
+        python-version: [3.8, 3.9, "3.10", "3.11"]
+    name: ${{ matrix.os }} - py${{ matrix.python-version }}
+    runs-on: ${{ matrix.os }}-latest
+    defaults:
+      run:
+        shell: bash
+    steps:
+      - name: Checkout repository
+        uses: actions/checkout@v4
+      - name: Setup Python ${{ matrix.python-version }}
+        uses: actions/setup-python@v5
+        with:
+          python-version: ${{ matrix.python-version }}
+          architecture: 'x64'
+      - name: Install dependencies
+        run: |
+          python -m pip install --progress-bar off --upgrade pip setuptools wheel
+          python -m pip install --progress-bar off .[build]
+      - name: Test package install
+        run: brainprint-sys_info
+      - name: Remove package install
+        run: python -m pip uninstall -yq brainprint
+      - name: Build package
+        run: python -m build
+      - name: Install sdist
+        run: pip install ./dist/*.tar.gz
+      - name: Test sdist install
+        run: brainprint-sys_info
+      - name: Remove sdist install
+        run: python -m pip uninstall -yq brainprint
+      - name: Install wheel
+        run: pip install ./dist/*.whl
+      - name: Test wheel install
+        run: brainprint-sys_info
+      - name: Remove wheel install
+        run: python -m pip uninstall -yq brainprint

junifer-0.0.8.dev193/junifer/external/BrainPrint/.github/workflows/code-style.yml

@@ -0,0 +1,44 @@
+name: code-style
+concurrency:
+  group: ${{ github.workflow }}-${{ github.event.number }}-${{ github.event.ref }}
+  cancel-in-progress: true
+on:
+  pull_request:
+  push:
+    branches: [main]
+  workflow_dispatch:
+
+jobs:
+  style:
+    timeout-minutes: 10
+    runs-on: ubuntu-latest
+    steps:
+      - name: Checkout repository
+        uses: actions/checkout@v4
+      - name: Setup Python 3.9
+        uses: actions/setup-python@v5
+        with:
+          python-version: '3.9'
+          architecture: 'x64'
+      - name: Install dependencies
+        run: |
+          python -m pip install --progress-bar off --upgrade pip setuptools wheel
+          python -m pip install --progress-bar off .[style]
+      - name: Run Ruff
+        run: ruff check .
+      - name: Run isort
+        uses: isort/isort-action@master
+      - name: Run black
+        uses: psf/black@stable
+        with:
+          options: "--check --verbose"
+          version: "23.10.1"
+      - name: Run codespell
+        uses: codespell-project/actions-codespell@master
+        with:
+          check_filenames: true
+          check_hidden: true
+          skip: './.git,./build,./.mypy_cache,./.pytest_cache'
+          ignore_words_file: ./.codespellignore
+      # - name: Run pydocstyle
+      #   run: pydocstyle .