From 79862cf8f5a137dfbe2e93900651cd2c938f9a2f Mon Sep 17 00:00:00 2001 From: Fede Raimondo Date: Wed, 4 Oct 2023 13:58:18 +0200 Subject: [PATCH 1/5] Update deps --- .../nilearn/junifer_nifti_spheres_masker.py | 4 +++ pyproject.toml | 30 +++++++++---------- 2 files changed, 19 insertions(+), 15 deletions(-) diff --git a/junifer/external/nilearn/junifer_nifti_spheres_masker.py b/junifer/external/nilearn/junifer_nifti_spheres_masker.py index d09320a19..1163d65af 100644 --- a/junifer/external/nilearn/junifer_nifti_spheres_masker.py +++ b/junifer/external/nilearn/junifer_nifti_spheres_masker.py @@ -397,6 +397,10 @@ class JuniferNiftiSpheresMasker(NiftiSpheresMasker): params = get_params(NiftiSpheresMasker, self) + # New in nilearn 0.10.1 + if hasattr(self, "clean_kwargs"): + params["clean_kwargs"] = self.clean_kwargs + signals, _ = self._cache( _filter_and_extract, ignore=["verbose", "memory", "memory_level"] )( diff --git a/pyproject.toml b/pyproject.toml index 3c5267e0f..674071cfb 100644 --- a/pyproject.toml +++ b/pyproject.toml @@ -40,15 +40,15 @@ classifiers = [ ] dependencies = [ "click>=8.1.3,<8.2", - "numpy>=1.24,<1.26", - "datalad>=0.15.4,<0.19", - "pandas>=1.4.0,<1.6", - "nibabel>=3.2.0,<4.1", - "nilearn>=0.9.0,<=0.10.0", - "sqlalchemy>=1.4.27,<= 1.5.0", + "numpy>=1.24,<1.27", + "datalad>=0.15.4,<0.20", + "pandas>=1.4.0,<2.2", + "nibabel>=3.2.0,<5.11", + "nilearn>=0.9.0,<=0.11.0", + "sqlalchemy>=1.4.27,<= 2.1.0", "ruamel.yaml>=0.17,<0.18", "importlib_metadata; python_version < '3.10'", - "h5py>=3.8.0,<3.9", + "h5py>=3.8.0,<3.10", ] dynamic = ["version"] @@ -63,15 +63,15 @@ junifer = "junifer.api.cli:cli" [project.optional-dependencies] dev = ["tox", "pre-commit"] docs = [ - "seaborn>=0.11.2,<0.12", - "Sphinx>=5.3.0,<5.4", - "sphinx-gallery>=0.11.0,<0.12", - "furo>=2022.9.29,<2023.0.0", + "seaborn>=0.11.2,<0.13", + "sphinx>=5.3.0,<7.3", + "sphinx-gallery>=0.11.0,<0.15.0", + "furo>=2022.9.29,<2023.10.0", "numpydoc>=1.5.0,<1.6", - "julearn==0.3.0", - "sphinx-copybutton==0.5.1", - "towncrier==22.12.0", - "sphinxcontrib-mermaid==0.8.1", + "julearn>=0.3.0,<0.4", + "sphinx-copybutton>=0.5.1,<0.5.3", + "towncrier>=22.12.0,<23.7", + "sphinxcontrib-mermaid>=0.8.1,<0.10", ] onthefly = ["bctpy==0.6.0"] -- 2.52.0 From 9ac2670d54bf1cd78693dcff3e68d1368bf373e5 Mon Sep 17 00:00:00 2001 From: Fede Raimondo Date: Wed, 4 Oct 2023 13:59:48 +0200 Subject: [PATCH 2/5] changelog --- docs/changes/newsfragments/253.change | 1 + 1 file changed, 1 insertion(+) create mode 100644 docs/changes/newsfragments/253.change diff --git a/docs/changes/newsfragments/253.change b/docs/changes/newsfragments/253.change new file mode 100644 index 000000000..43f38ef69 --- /dev/null +++ b/docs/changes/newsfragments/253.change @@ -0,0 +1 @@ +Update dependencies requirements by `Fede Raimondo`_ -- 2.52.0 From e00b6f38aeb60f07856728e5d3bb7988eefc765c Mon Sep 17 00:00:00 2001 From: Fede Raimondo Date: Wed, 4 Oct 2023 14:03:53 +0200 Subject: [PATCH 3/5] fix codespell --- docs/contribution.rst | 2 +- ignore_words.txt | 1 + 2 files changed, 2 insertions(+), 1 deletion(-) diff --git a/docs/contribution.rst b/docs/contribution.rst index 63bb14266..15fad6ec9 100644 --- a/docs/contribution.rst +++ b/docs/contribution.rst @@ -171,7 +171,7 @@ Writing Examples The format used for text is reST. Check the `sphinx reST reference`_ for more details. The examples are run and displayed in HTML format using `sphinx gallery`_. To add an example, just create a ``.py`` file that starts -either with ``plot_`` or ``run_``, dependending on whether the example generates +either with ``plot_`` or ``run_``, depending on whether the example generates a figure or not. The first lines of the example should be a Python block comment with a title, diff --git a/ignore_words.txt b/ignore_words.txt index 1ac8c4893..d333dfe52 100644 --- a/ignore_words.txt +++ b/ignore_words.txt @@ -2,3 +2,4 @@ master nin chang sepulcre +arange \ No newline at end of file -- 2.52.0 From 788225a26b47de3d596003d0eb3a4e8ca8fcb00c Mon Sep 17 00:00:00 2001 From: Fede Raimondo Date: Wed, 4 Oct 2023 14:08:39 +0200 Subject: [PATCH 4/5] Change conda-env + docs + changes --- conda-env.yml | 34 +++++++++---------- .../newsfragments/{253.change => 253.misc} | 0 docs/installation.rst | 14 ++++---- 3 files changed, 24 insertions(+), 24 deletions(-) rename docs/changes/newsfragments/{253.change => 253.misc} (100%) diff --git a/conda-env.yml b/conda-env.yml index fceb24902..8fd38762c 100644 --- a/conda-env.yml +++ b/conda-env.yml @@ -3,23 +3,23 @@ channels: - conda-forge - defaults dependencies: - - python=3.10 + - python>=3.10,<=3.11 - click=8.1.* - - numpy>=1.22,<1.24 - - pandas>=1.4.0,<1.6 - - nibabel>=3.2.0,<4.1 - - nilearn>=0.9.0,<=0.10.0 - - sqlalchemy>=1.4.27,<= 1.5.0 + - numpy>=1.22,<1.27 + - pandas>=1.4.0,<2.2 + - nibabel>=3.2.0,<5.2 + - nilearn>=0.9.0,<=0.10.1 + - sqlalchemy>=1.4.27,<= 2.0.21 - ruamel.yaml=0.17.* - - h5py=3.8.* - - seaborn=0.11.* - - Sphinx=5.3.* - - sphinx-gallery=0.11.* - - furo>=2022.9.29,<2023.0.0 - - numpydoc=1.5.* - - sphinx-copybutton=0.5.* - - towncrier=22.12.* - - sphinxcontrib-mermaid=0.8.* + - h5py>=3.8,<=3.9 + - seaborn>=0.11,<=0.13 + - sphinx>=5.3,<7.3 + - sphinx-gallery>=0.11.0,<0.15.0 + - furo>=2022.9.29,<2023.10.0 + - numpydoc>=1.5.0,<1.6 + - phinx-copybutton>=0.5.1,<0.5.3 + - towncrier>=22.12.0,<23.7 + - sphinxcontrib-mermaid>=0.8.1,<0.10 - tox - ipykernel - pytest-cov @@ -29,5 +29,5 @@ dependencies: - codespell - pip - pip: - - datalad>=0.15.4,<0.19 - - julearn==0.2.5 + - datalad>=0.15.4,<0.20 + - julearn==0.3.0 diff --git a/docs/changes/newsfragments/253.change b/docs/changes/newsfragments/253.misc similarity index 100% rename from docs/changes/newsfragments/253.change rename to docs/changes/newsfragments/253.misc diff --git a/docs/installation.rst b/docs/installation.rst index f89363c2c..709d9fd82 100644 --- a/docs/installation.rst +++ b/docs/installation.rst @@ -10,14 +10,14 @@ Requirements junifer is compatible with `Python`_ >= 3.8 and requires the following packages: * ``click>=8.1.3,<8.2`` -* ``numpy>=1.22,<1.24`` -* ``datalad>=0.15.4,<0.19`` -* ``pandas>=1.4.0,<1.6`` -* ``nibabel>=3.2.0,<4.1`` -* ``nilearn>=0.9.0,<=0.10.0`` -* ``sqlalchemy>=1.4.27,<= 1.5.0`` +* ``numpy>=1.24,<1.27`` +* ``datalad>=0.15.4,<0.20`` +* ``pandas>=1.4.0,<2.2`` +* ``nibabel>=3.2.0,<5.11`` +* ``nilearn>=0.9.0,<=0.11.0`` +* ``sqlalchemy>=1.4.27,<= 2.1.0`` * ``ruamel.yaml>=0.17,<0.18`` -* ``h5py>=3.8.0,<3.9`` +* ``h5py>=3.8.0,<3.10`` Depending on the installation method, these packages might be installed automatically. -- 2.52.0 From 9b25866ffa0e40aff245664a2d1e67b0a19e5a14 Mon Sep 17 00:00:00 2001 From: Fede Raimondo Date: Wed, 4 Oct 2023 14:12:24 +0200 Subject: [PATCH 5/5] typo --- conda-env.yml | 2 +- 1 file changed, 1 insertion(+), 1 deletion(-) diff --git a/conda-env.yml b/conda-env.yml index 8fd38762c..f50aa5330 100644 --- a/conda-env.yml +++ b/conda-env.yml @@ -17,7 +17,7 @@ dependencies: - sphinx-gallery>=0.11.0,<0.15.0 - furo>=2022.9.29,<2023.10.0 - numpydoc>=1.5.0,<1.6 - - phinx-copybutton>=0.5.1,<0.5.3 + - sphinx-copybutton>=0.5.1,<0.5.3 - towncrier>=22.12.0,<23.7 - sphinxcontrib-mermaid>=0.8.1,<0.10 - tox -- 2.52.0