From 1ba8c758291907ab854ff4cb85b382ac774f445a Mon Sep 17 00:00:00 2001 From: Chris Markiewicz Date: Tue, 14 Nov 2023 00:31:45 -0500 Subject: [PATCH 1/2] MNT: Shift more config into env.yml --- Dockerfile | 5 ++--- env.yml | 5 +++++ 2 files changed, 7 insertions(+), 3 deletions(-) diff --git a/Dockerfile b/Dockerfile index cc389d914..cce660bbd 100644 --- a/Dockerfile +++ b/Dockerfile @@ -103,6 +103,8 @@ RUN curl -Ls https://micro.mamba.pm/api/micromamba/linux-64/latest | tar -xvj bi ENV MAMBA_ROOT_PREFIX="/opt/conda" COPY env.yml /tmp/env.yml +COPY requirements.txt /tmp/requirements.txt +WORKDIR /tmp RUN micromamba create -y -f /tmp/env.yml && \ micromamba clean -y -a @@ -110,9 +112,6 @@ ENV PATH="/opt/conda/envs/fmriprep/bin:$PATH" RUN /opt/conda/envs/fmriprep/bin/npm install -g svgo@^2.8 bids-validator@1.11.0 && \ rm -r ~/.npm -COPY requirements.txt /tmp/requirements.txt -RUN /opt/conda/envs/fmriprep/bin/pip install --no-cache-dir -r /tmp/requirements.txt - # # Main stage # diff --git a/env.yml b/env.yml index a36a8a16b..c96ee9411 100644 --- a/env.yml +++ b/env.yml @@ -35,3 +35,8 @@ dependencies: - fsl-mcflirt=2111.0 - fsl-miscmaths=2203.2 - fsl-topup=2203.1 + - pip + - pip: + - -r requirements.txt +variables: + FSLOUTPUTTYPE: NIFTI_GZ From 50ac3f15b34200b32b382b1b569dcc1ba5d89c2a Mon Sep 17 00:00:00 2001 From: Chris Markiewicz Date: Tue, 14 Nov 2023 00:55:47 -0500 Subject: [PATCH 2/2] MNT: Bump environment --- env.yml | 16 +++++----- requirements.txt | 76 +++++++++++++++++++++++------------------------- 2 files changed, 44 insertions(+), 48 deletions(-) diff --git a/env.yml b/env.yml index c96ee9411..10efd8e26 100644 --- a/env.yml +++ b/env.yml @@ -17,7 +17,7 @@ dependencies: - scipy=1.11 - matplotlib=3.8 - pandas=2.1 - - h5py=3.8 + - h5py=3.10 # Dependencies compiled against numpy, best to stick with conda - nitime=0.10 - scikit-image=0.22 @@ -26,15 +26,15 @@ dependencies: - graphviz=6.0 - pandoc=3.1 # Workflow dependencies: ANTs - - ants=2.4.4 - # Workflow dependencies: FSL (versions pinned in 6.0.6.2) - - fsl-bet2=2111.0 - - fsl-flirt=2111.0 - - fsl-fast4=2111.0 - - fsl-fugue=2201.2 + - ants=2.5.0 + # Workflow dependencies: FSL (versions pinned in 6.0.7.4) + - fsl-bet2=2111.4 + - fsl-flirt=2111.2 + - fsl-fast4=2111.3 + - fsl-fugue=2201.3 - fsl-mcflirt=2111.0 - fsl-miscmaths=2203.2 - - fsl-topup=2203.1 + - fsl-topup=2203.2 - pip - pip: - -r requirements.txt diff --git a/requirements.txt b/requirements.txt index e7a880961..fd7e75174 100644 --- a/requirements.txt +++ b/requirements.txt @@ -2,9 +2,9 @@ # This file is autogenerated by pip-compile with Python 3.10 # by the following command: # -# pip-compile --extra=container +# pip-compile --extra=container --strip-extras # -annexremote==1.6.0 +annexremote==1.6.4 # via # datalad # datalad-next @@ -35,7 +35,7 @@ cffi==1.16.0 # via cryptography chardet==5.2.0 # via datalad -charset-normalizer==3.3.0 +charset-normalizer==3.3.2 # via requests ci-info==0.3.0 # via @@ -50,20 +50,18 @@ codecarbon==2.3.1 # via # fmriprep # fmriprep (pyproject.toml) -contourpy==1.1.1 +contourpy==1.2.0 # via matplotlib -cryptography==41.0.4 +cryptography==41.0.5 # via secretstorage cycler==0.12.1 # via matplotlib -cython==3.0.3 - # via nitime datalad==0.19.3 # via # datalad-next # datalad-osf # fmriprep (pyproject.toml) -datalad-next==1.0.0 +datalad-next==1.0.2 # via datalad-osf datalad-osf==0.3.0 # via fmriprep (pyproject.toml) @@ -71,21 +69,21 @@ distro==1.8.0 # via datalad docopt==0.6.2 # via num2words -etelemetry==0.3.0 +etelemetry==0.3.1 # via nipype fasteners==0.19 # via datalad -filelock==3.12.4 +filelock==3.13.1 # via nipype -fonttools==4.43.1 +fonttools==4.44.0 # via matplotlib formulaic==0.5.2 # via pybids fuzzywuzzy==0.18.0 # via codecarbon -greenlet==3.0.0 +greenlet==3.0.1 # via sqlalchemy -h5py==3.8.0 +h5py==3.10.0 # via nitransforms humanize==4.8.0 # via @@ -93,15 +91,16 @@ humanize==4.8.0 # datalad-next idna==3.4 # via requests -imageio==2.31.5 +imageio==2.32.0 # via scikit-image importlib-metadata==6.8.0 # via keyring -importlib-resources==6.1.0 +importlib-resources==6.1.1 # via # niworkflows # sdcflows -indexed-gzip==1.8.5 + # templateflow +indexed-gzip==1.8.7 # via smriprep interface-meta==1.3.0 # via formulaic @@ -126,7 +125,7 @@ joblib==1.3.2 # via # nilearn # scikit-learn -keyring==24.2.0 +keyring==24.3.0 # via datalad keyrings-alt==5.0.0 # via datalad @@ -149,11 +148,11 @@ lxml==4.9.3 # nilearn # prov # svgutils -mapca==0.0.3 +mapca==0.0.4 # via tedana markupsafe==2.1.3 # via jinja2 -matplotlib==3.8.0 +matplotlib==3.8.1 # via # nireports # nitime @@ -167,10 +166,9 @@ more-itertools==10.1.0 # via jaraco-classes msgpack==1.0.7 # via datalad -networkx==3.1 +networkx==3.2.1 # via # nipype - # nitime # prov # scikit-image nibabel==5.1.0 @@ -181,7 +179,6 @@ nibabel==5.1.0 # nilearn # nipype # nireports - # nitime # nitransforms # niworkflows # pybids @@ -206,7 +203,7 @@ nireports==23.1.0 # via # fmriprep # fmriprep (pyproject.toml) -nitime==0.10.1 +nitime==0.10.2 # via # fmriprep # fmriprep (pyproject.toml) @@ -222,9 +219,9 @@ niworkflows==1.8.1 # fmriprep (pyproject.toml) # sdcflows # smriprep -num2words==0.5.12 +num2words==0.5.13 # via pybids -numpy==1.26.0 +numpy==1.26.2 # via # bokeh # contourpy @@ -258,6 +255,7 @@ packaging==23.2 # via # bokeh # datalad + # etelemetry # fmriprep # fmriprep (pyproject.toml) # matplotlib @@ -267,7 +265,7 @@ packaging==23.2 # niworkflows # scikit-image # smriprep -pandas==2.1.1 +pandas==2.1.3 # via # codecarbon # fmriprep @@ -279,7 +277,7 @@ pandas==2.1.1 # pybids # seaborn # tedana -patool==1.12 +patool==1.15.0 # via datalad pillow==10.0.1 # via @@ -287,13 +285,13 @@ pillow==10.0.1 # imageio # matplotlib # scikit-image -platformdirs==3.11.0 +platformdirs==4.0.0 # via datalad -prometheus-client==0.17.1 +prometheus-client==0.18.0 # via codecarbon prov==2.0.0 # via nipype -psutil==5.9.5 +psutil==5.9.6 # via # codecarbon # fmriprep @@ -328,7 +326,7 @@ python-dateutil==2.8.2 # nipype # pandas # prov -python-gitlab==3.15.0 +python-gitlab==4.1.1 # via datalad pytz==2023.3.post1 # via @@ -362,7 +360,7 @@ scikit-image==0.22.0 # via # niworkflows # sdcflows -scikit-learn==1.3.1 +scikit-learn==1.3.2 # via # mapca # nilearn @@ -391,7 +389,7 @@ seaborn==0.13.0 # niworkflows secretstorage==3.3.3 # via keyring -sentry-sdk==1.32.0 +sentry-sdk==1.35.0 # via fmriprep simplejson==3.19.2 # via nipype @@ -405,7 +403,7 @@ smriprep==0.12.2 # via # fmriprep # fmriprep (pyproject.toml) -sqlalchemy==2.0.21 +sqlalchemy==2.0.23 # via pybids svgutils==0.3.4 # via @@ -415,7 +413,7 @@ tedana==23.0.1 # via # fmriprep # fmriprep (pyproject.toml) -templateflow==23.0.0 +templateflow==23.1.0 # via # fmriprep # fmriprep (pyproject.toml) @@ -457,15 +455,13 @@ typing-extensions==4.8.0 # sqlalchemy tzdata==2023.3 # via pandas -tzlocal==5.1 +tzlocal==5.2 # via apscheduler -urllib3==2.0.6 +urllib3==2.1.0 # via # requests # sentry-sdk -wrapt==1.15.0 +wrapt==1.16.0 # via formulaic -www-authenticate==0.9.2 - # via datalad-next zipp==3.17.0 # via importlib-metadata