Merge pull request #798 from effigies/mnt/1.3.x/pip-compile

MNT: Create a requirements.txt to keep the LTS branch buildable

Author: effigies

.circleci/config.yml

@@ -1,6 +1,7 @@
 version: 2.1
 orbs:
   docker: circleci/[email protected]
+  codecov: codecov/[email protected]
 
 jobs:
   build:
@@ -117,7 +118,6 @@ jobs:
 
       - restore_cache:
           keys:
-            - data-v3-{{ .Branch }}-{{ epoch }}
             - data-v3-{{ .Branch }}-
             - data-v3-maint/1.3.x-
             - data-v3-master-
@@ -222,9 +222,6 @@ jobs:
     steps:
       - attach_workspace:
           at: /tmp
-      - run:
-          name: Get codecov
-          command: python -m pip install codecov
       - restore_cache:
           keys:
             - build-v1-{{ .Branch }}-{{ .Revision }}
@@ -254,7 +251,7 @@ jobs:
 
       - restore_cache:
           keys:
-            - data-v3-{{ .Branch }}-{{ epoch }}
+            - data-v3-{{ .Branch }}-
 
       - run:
           name: Run unit tests
@@ -274,12 +271,9 @@ jobs:
                      --ignore=niworkflows/func/tests/ \
                      niworkflows/
 
-      - run:
-          name: Submit unit test coverage
-          command: |
-            cd /tmp/src/niworkflows
-            python -m codecov --file /tmp/tests/summaries/unittests.xml \
-                --flags unittests -e CIRCLE_JOB
+      - codecov/upload:
+          file: /tmp/tests/summaries/unittests.xml
+          flags: unittests
 
       - run:
           name: Run reportlet tests
@@ -294,12 +288,10 @@ jobs:
               pytest -n auto --junit-xml=/tmp/summaries/reportlets.xml \
                      --cov niworkflows --cov-report xml:/tmp/summaries/reportlets.xml \
                      niworkflows/tests/
-      - run:
-          name: Submit reportlet test coverage
-          command: |
-            cd /tmp/src/niworkflows
-            python -m codecov --file /tmp/tests/summaries/reportlets.xml \
-                --flags reportlettests -e CIRCLE_JOB
+
+      - codecov/upload:
+          file: /tmp/tests/summaries/reportlets.xml
+          flags: reportlettests
 
       - run:
           name: Clean up tests directory
@@ -339,7 +331,7 @@ jobs:
 
       - restore_cache:
           keys:
-            - build-v1-{{ .Branch }}-{{ epoch }}
+            - build-v1-{{ .Branch }}-
       - run:
           name: Docker authentication
           command: |
@@ -367,7 +359,6 @@ jobs:
             docker tag localhost:5000/niworkflows niworkflows:latest
       - restore_cache:
           keys:
-            - masks-workdir-v3-{{ .Branch }}-{{epoch}}
             - masks-workdir-v3-{{ .Branch }}-
             - masks-workdir-v3-maint/1.3.x-
             - masks-workdir-v3-master-
@@ -417,16 +408,10 @@ jobs:
               -e COVERAGE_FILE=/tmp/masks/reports/.coverage \
               -v /tmp/masks/reports:/tmp/masks/reports \
               niworkflows:latest coverage xml -o coverage.xml
-      - run:
-          name: Get codecov
-          command: python -m pip install codecov
-      - run:
-          name: Submit masks test coverage
-          working_directory: /tmp/src/niworkflows
-          command: |
-            cp /tmp/masks/reports/coverage.xml .
-            sed -i "s+/src/niworkflows+/tmp/src/niworkflows+g" coverage.xml
-            python -m codecov --file coverage.xml --flags masks -e CIRCLE_JOB
+
+      - codecov/upload:
+          file: /tmp/tests/summaries/unittests.xml
+          flags: masks
 
   test_package:
     docker:

Dockerfile

@@ -151,7 +151,7 @@ COPY . /src/niworkflows/
 ARG VERSION
 RUN echo "${VERSION}" > /src/niworkflows/niworkflows/VERSION && \
     echo "include niworkflows/VERSION" >> /src/niworkflows/MANIFEST.in && \
-    pip install --no-cache-dir -e .[all] && \
+    pip install --no-cache-dir -r requirements.txt -e .[all] && \
     rm -rf $HOME/.cache/pip
 
 COPY docker/files/nipype.cfg /home/niworkflows/.nipype/nipype.cfg

niworkflows/interfaces/utils.py

@@ -956,7 +956,7 @@ def less_breakable(a_string):
     drop_columns = drop_columns or []
     additional_metadata = additional_metadata or {}
     try:
-        tsv_data = pd.read_csv(in_tsv, "\t")
+        tsv_data = pd.read_csv(in_tsv, sep="\t")
     except pd.errors.EmptyDataError:
         tsv_data = pd.DataFrame()
     for k, v in additional_metadata.items():

requirements.in

@@ -0,0 +1,29 @@
+# Hints to pip-compile that combine the requirements in setup.cfg
+# and the environment pinned in fMRIPrep 20.2.x's docker/files/environment.yml
+#
+# Some dependencies need old versions of setuptools to resolve. The following environment
+# currently builds:
+#
+#  python==3.7 pip-tools setuptools<58
+#
+attrs
+jinja2
+h5py==3.5
+matplotlib==2.2.2
+nibabel >= 3.0.1
+nilearn == 0.7
+nipype >= 1.5.1, != 1.7.0
+nitransforms >= 20.0.0rc3,<20.2
+numpy==1.19
+packaging
+pandas==0.24
+pybids >= 0.11.1, < 0.15
+PyYAML
+scikit-image
+scikit-learn==0.21
+scipy==1.5
+seaborn==0.11.2
+svgutils == 0.3.1
+templateflow >= 0.6,<23
+traits==4.6.0
+transforms3d

requirements.txt

@@ -0,0 +1,217 @@
+#
+# This file is autogenerated by pip-compile with Python 3.7
+# by the following command:
+#
+#    pip-compile --resolver=backtracking
+#
+astor==0.8.1
+    # via formulaic
+attrs==22.2.0
+    # via -r requirements.in
+bids-validator==1.11.0
+    # via pybids
+cached-property==1.5.2
+    # via h5py
+certifi==2022.12.7
+    # via requests
+charset-normalizer==3.1.0
+    # via requests
+ci-info==0.3.0
+    # via etelemetry
+click==8.1.3
+    # via
+    #   nipype
+    #   pybids
+cycler==0.11.0
+    # via matplotlib
+docopt==0.6.2
+    # via num2words
+etelemetry==0.3.0
+    # via nipype
+filelock==3.11.0
+    # via nipype
+formulaic==0.2.4
+    # via pybids
+h5py==3.5.0
+    # via
+    #   -r requirements.in
+    #   nitransforms
+idna==3.4
+    # via requests
+imageio==2.27.0
+    # via scikit-image
+importlib-metadata==4.13.0
+    # via
+    #   click
+    #   rdflib
+interface-meta==1.3.0
+    # via formulaic
+isodate==0.6.1
+    # via rdflib
+jinja2==3.1.2
+    # via -r requirements.in
+joblib==1.2.0
+    # via
+    #   nilearn
+    #   scikit-learn
+kiwisolver==1.4.4
+    # via matplotlib
+looseversion==1.1.2
+    # via nipype
+lxml==4.9.2
+    # via
+    #   prov
+    #   svgutils
+markupsafe==2.1.2
+    # via jinja2
+matplotlib==2.2.2
+    # via
+    #   -r requirements.in
+    #   seaborn
+networkx==2.6.3
+    # via
+    #   nipype
+    #   prov
+    #   scikit-image
+nibabel==4.0.2
+    # via
+    #   -r requirements.in
+    #   nilearn
+    #   nipype
+    #   nitransforms
+    #   pybids
+nilearn==0.7.0
+    # via -r requirements.in
+nipype==1.8.6
+    # via -r requirements.in
+nitransforms==20.0.0rc5
+    # via -r requirements.in
+num2words==0.5.12
+    # via pybids
+numpy==1.19.0
+    # via
+    #   -r requirements.in
+    #   formulaic
+    #   h5py
+    #   imageio
+    #   matplotlib
+    #   nibabel
+    #   nilearn
+    #   nipype
+    #   nitransforms
+    #   pandas
+    #   pybids
+    #   pywavelets
+    #   scikit-image
+    #   scikit-learn
+    #   scipy
+    #   seaborn
+    #   tifffile
+packaging==23.1
+    # via
+    #   -r requirements.in
+    #   nibabel
+    #   nipype
+    #   scikit-image
+pandas==0.24.0
+    # via
+    #   -r requirements.in
+    #   formulaic
+    #   nilearn
+    #   pybids
+    #   seaborn
+pillow==9.5.0
+    # via
+    #   imageio
+    #   scikit-image
+prov==2.0.0
+    # via nipype
+pybids==0.14.1
+    # via
+    #   -r requirements.in
+    #   templateflow
+pydot==1.4.2
+    # via nipype
+pyparsing==3.0.9
+    # via
+    #   matplotlib
+    #   pydot
+    #   rdflib
+python-dateutil==2.8.2
+    # via
+    #   matplotlib
+    #   nipype
+    #   pandas
+    #   prov
+pytz==2023.3
+    # via
+    #   matplotlib
+    #   pandas
+pywavelets==1.3.0
+    # via scikit-image
+pyyaml==6.0
+    # via -r requirements.in
+rdflib==6.3.2
+    # via
+    #   nipype
+    #   prov
+requests==2.28.2
+    # via
+    #   etelemetry
+    #   nilearn
+    #   templateflow
+scikit-image==0.19.3
+    # via -r requirements.in
+scikit-learn==0.21.0
+    # via
+    #   -r requirements.in
+    #   nilearn
+scipy==1.5.0
+    # via
+    #   -r requirements.in
+    #   formulaic
+    #   nilearn
+    #   nipype
+    #   nitransforms
+    #   pybids
+    #   scikit-image
+    #   scikit-learn
+    #   seaborn
+seaborn==0.11.2
+    # via -r requirements.in
+simplejson==3.19.1
+    # via nipype
+six==1.16.0
+    # via
+    #   isodate
+    #   matplotlib
+    #   python-dateutil
+sqlalchemy==1.3.24
+    # via pybids
+svgutils==0.3.1
+    # via -r requirements.in
+templateflow==0.8.1
+    # via -r requirements.in
+tifffile==2021.11.2
+    # via scikit-image
+tqdm==4.65.0
+    # via templateflow
+traits==4.6.0
+    # via
+    #   -r requirements.in
+    #   nipype
+transforms3d==0.4.1
+    # via -r requirements.in
+typing-extensions==4.5.0
+    # via
+    #   importlib-metadata
+    #   kiwisolver
+urllib3==1.26.15
+    # via requests
+wrapt==1.15.0
+    # via formulaic
+zipp==3.15.0
+    # via importlib-metadata
+
+# The following packages are considered to be unsafe in a requirements file:
+# setuptools