Merge pull request #104 from poldracklab/fix/packaging-tests

MAINT: Revise tests and Docker image dependencies

.circleci/config.yml

@@ -45,7 +45,7 @@ jobs:
           name: Prepare a Python environment
           command: |
               pyenv local 3.7.0
-              python3 -m pip install "setuptools ~= 42.0" "setuptools_scm[toml] >= 3.4" "pip>=10.0.1"
+              python3 -m pip install "setuptools >= 45.0" "setuptools_scm[toml] >= 3.4" "pip>=10.0.1"
       - run:
           name: Build Docker image & push to registry
           no_output_timeout: 60m
@@ -154,7 +154,7 @@ jobs:
           command: |
             python3 -m venv /tmp/buildenv
             source /tmp/buildenv/bin/activate
-            python3 -m pip install "setuptools ~= 42.0" wheel "setuptools_scm[toml] >= 3.4" \
+            python3 -m pip install "setuptools >= 45.0" wheel "setuptools_scm[toml] >= 3.4" \
                 "pip>=10.0.1" twine docutils
             python setup.py sdist bdist_wheel
             twine check dist/nitransforms*
@@ -168,7 +168,7 @@ jobs:
           command: |
             python3 -m venv /tmp/install_sdist
             source /tmp/install_sdist/bin/activate
-            python3 -m pip install "setuptools ~= 42.0" "pip>=10.0.1"
+            python3 -m pip install "setuptools >= 45.0" "pip>=10.0.1"
 
             THISVERSION=$( python3 setup.py --version )
             THISVERSION=${CIRCLE_TAG:-$THISVERSION}
@@ -182,7 +182,7 @@ jobs:
           command: |
             python3 -m venv /tmp/install_wheel
             source /tmp/install_wheel/bin/activate
-            python3 -m pip install "setuptools ~= 42.0" "pip>=10.0.1"
+            python3 -m pip install "setuptools >= 45.0" "pip>=10.0.1"
 
             THISVERSION=$( python3 setup.py --version )
             THISVERSION=${CIRCLE_TAG:-$THISVERSION}

.dockerignore

@@ -0,0 +1,86 @@
+joss/
+.github/
+.circle/
+
+# Byte-compiled / optimized / DLL files
+__pycache__/
+*.py[cod]
+*$py.class
+.pytest_cache/
+
+# C extensions
+*.so
+*.c
+
+# Distribution / packaging
+.Python
+env/
+# build/ # commented due to some strangeness with Docker/circle setup
+develop-eggs/
+dist/
+build/lib*
+build/temp*
+downloads/
+eggs/
+.eggs/
+lib/
+lib64/
+parts/
+sdist/
+var/
+*.egg-info/
+.installed.cfg
+*.egg
+
+# PyInstaller
+#  Usually these files are written by a python script from a template
+#  before PyInstaller builds the exe, so as to inject date/other infos into it.
+*.manifest
+*.spec
+
+# Installer logs
+pip-log.txt
+pip-delete-this-directory.txt
+
+# Unit test / coverage reports
+htmlcov/
+.tox/
+.coverage
+.coverage.*
+.cache
+nosetests.xml
+coverage.xml
+*,cover
+.hypothesis/
+.pep8speaks.yml
+
+# Translations
+*.mo
+*.pot
+
+# Django stuff:
+*.log
+
+# Sphinx documentation
+docs/_build/
+build/
+
+# PyBuilder
+target/
+
+#Ipython Notebook
+.ipynb_checkpoints
+
+# pycharm project settings
+.idea
+
+# Spyder project settings
+.spyderproject
+.spyproject
+
+auth/
+secrets.py
+local_settings.py
+
+*.swp
+.vscode/

Dockerfile

@@ -86,10 +86,11 @@ ENV FSLDIR="/usr/share/fsl/5.0" \
     AFNI_PLUGINPATH="/usr/lib/afni/plugins"
 ENV PATH="/usr/lib/fsl/5.0:/usr/lib/afni/bin:$PATH"
 
-# Installing ANTs 2.2.0 (NeuroDocker build)
+# Installing ANTs 2.3.3 (NeuroDocker build)
+# Note: the URL says 2.3.4 but it is actually 2.3.3
 ENV ANTSPATH=/usr/lib/ants
 RUN mkdir -p $ANTSPATH && \
-    curl -sSL "https://dl.dropbox.com/s/2f4sui1z6lcgyek/ANTs-Linux-centos5_x86_64-v2.2.0-0740f91.tar.gz" \
+    curl -sSL "https://dl.dropbox.com/s/gwf51ykkk5bifyj/ants-Linux-centos6_x86_64-v2.3.4.tar.gz" \
     | tar -xzC $ANTSPATH --strip-components 1
 ENV PATH=$ANTSPATH:$PATH
 
@@ -106,14 +107,18 @@ ENV PATH="/usr/local/miniconda/bin:$PATH" \
     PYTHONNOUSERSITE=1
 
 # Installing precomputed python packages
-RUN conda install -y python=3.7.1 \
-                     pip=19.1 \
-                     mkl=2018.0.3 \
+RUN conda install -y -c anaconda -c conda-forge \
+                     python=3.7 \
+                     libxml2=2.9 \
+                     libxslt=1.1 \
+                     mkl \
                      mkl-service \
-                     numpy=1.15.4 \
-                     scipy=1.1.0 \
-                     libxml2=2.9.8 \
-                     libxslt=1.1.32 \
+                     numpy=1.20 \
+                     pip=21 \
+                     scipy=1.6 \
+                     setuptools \
+                     setuptools_scm \
+                     toml \
                      zlib; sync && \
     chmod -R a+rX /usr/local/miniconda; sync && \
     chmod +x /usr/local/miniconda/bin/*; sync && \

pyproject.toml

@@ -1,5 +1,5 @@
 [build-system]
-requires = ["setuptools ~= 42.0", "wheel", "setuptools_scm[toml] >= 3.4"]
+requires = ["setuptools >= 42.0", "wheel", "setuptools_scm[toml] >= 3.4", "setuptools_scm_git_archive"]
 
 [tool.setuptools_scm]
 write_to = "nitransforms/_version.py"

setup.cfg

@@ -6,9 +6,9 @@ classifiers =
     Intended Audience :: Science/Research
     Topic :: Scientific/Engineering :: Image Recognition
     License :: OSI Approved :: BSD License
-    Programming Language :: Python :: 3.6
     Programming Language :: Python :: 3.7
     Programming Language :: Python :: 3.8
+    Programming Language :: Python :: 3.9
 description = NiTransforms -- Neuroimaging spatial transforms in Python.
 license = MIT License
 long_description = file:README.md
@@ -20,7 +20,7 @@ project_urls =
 url = https://github.com/poldracklab/nitransforms
 
 [options]
-python_requires = >= 3.6
+python_requires = >= 3.7
 install_requires =
     numpy
     scipy