Upgrade to Python 3.7 (#592)

* added notes on issues upgrading to py37

* added changes

* changed rtd python version

* added spatial_lda and palettable

* added spatial_lda

* pycodestyle

* removed unnecessary file

* palettable

* removed tables from setup.py

* changed spatial-lda from 0.1.3 to 0.1.2

* dropped scikit image from 0.16.2 to 0.14.3

* changed python 3.7 -> 3.7.12 in .travis.yml

* changed python 3.7.12 -> 3.7 in .travis.yml

* removed spatial_lda dependency_links

* uncommented dep links

* adjsuted spatial_lda requirements

* depricated importlib-metadata from 4.11.4 to 3.6.0

* adjusted requirements

* setuptools==60.8.2

* importlib-metadata<3.4.0

* removed importlib_metadata requirements

* moved setuptools to the top of req.txt

* what version of setuptools and importlib-metadata is travis-ci using?

* updated travis' setuptools / importlib-metadata

* updated travis

* reverted scikit-image to 14.3

* replaced instances of 3.6 in conf.py, start_docker.sh, and dev.md with 3.7

* spelling

* Update docs/_rtd/development.md

Co-authored-by: Noah F. Greenwald <noahfgreenwald@gmail.com>

* removed spatial_lda@primary

* added toffy stile dependency retrieval

* bumped matplotlib, ipympl, should work better with 3.8 libraries: toffy, mibi-bin-tools

* make_iterable now accounts for instances of T, s.t. type(T) == `type`

* updated VERSION from 0.2.10 -> 0.3.00

Co-authored-by: Sricharan Reddy Varra <srivarra@mbp.local>
Co-authored-by: Sricharan Reddy Varra <srivarra@DN52eo49.SUNet>
Co-authored-by: Noah F. Greenwald <noahfgreenwald@gmail.com>

.readthedocs.yml

@@ -5,6 +5,6 @@ sphinx:
   fail_on_warning: true
 
 python:
-  version: 3.6
+  version: "3.7"
   install:
     - requirements: docs/rtd-requirements.txt

.travis.yml

@@ -6,10 +6,13 @@ git:
 language: python
 
 python:
-  - 3.6
+  - 3.7
 
+# Install the updated versions of importlib-metadata and setuptools, as Travis 3.7 environments
+# contains a very old version of importlib-metadata which is incompatible for 3.7+
 # We add python path to enable testing jupyter notebooks
 install:
+  - pip install -U importlib_metadata setuptools
   - travis_retry pip install -r requirements.txt
   - travis_retry pip install -r requirements-test.txt
   - travis_retry export PYTHONPATH=$PWD
@@ -26,7 +29,7 @@ script:
 jobs:
   include:
     - stage: pypi_deploy
-      python: 3.6
+      python: 3.7
       deploy:
         provider: pypi
         user: $PYPI_USERNAME
@@ -35,7 +38,7 @@ jobs:
           tags: true
     - stage: docker_deploy
       if: tag IS present
-      python: 3.6
+      python: 3.7
       script:
         - "travis_wait 120 sleep 7200 &"
         - echo "$DOCKER_PASSWORD" | docker login -u "$DOCKER_USERNAME" --password-stdin 

Dockerfile

@@ -1,4 +1,4 @@
-FROM python:3.6
+FROM python:3.7
 
 # system maintenance
 RUN apt-get update

ark/segmentation/marker_quantification.py

@@ -114,13 +114,19 @@ def assign_single_compartment_features(marker_counts, compartment, cell_props, c
     cell_counts = EXTRACTION_FUNCTION[extraction](cell_coords, input_images, **kwargs)
 
     # get morphology metrics
-    current_cell_props = cell_props.loc[cell_props['label'] == label_id, regionprops_names]
+    # Filter regionprops_names to only those in cell_props.columns
+    filtered_regionprops_names = [rp_name for rp_name in regionprops_names if rp_name in
+                                  cell_props.columns]
+    current_cell_props = cell_props.loc[cell_props['label'] == label_id,
+                                        filtered_regionprops_names]
 
     # combine marker counts and morphology metrics together
     cell_features = np.concatenate((cell_counts, current_cell_props), axis=None)
 
     # add counts of each marker to appropriate column
-    marker_counts.loc[compartment, cell_id, marker_counts.features[1]:] = cell_features
+    # Only include the marker_count features up to the last filtered feature.
+    marker_counts.loc[compartment, cell_id,
+                      marker_counts.features[1]:filtered_regionprops_names[-1]] = cell_features
 
     # add cell size to first column
     marker_counts.loc[compartment, cell_id, marker_counts.features[0]] = cell_coords.shape[0]

ark/utils/misc_utils.py

@@ -1,4 +1,5 @@
 import os
+from typing import Any
 import warnings
 from collections.abc import Iterable
 import numpy as np
@@ -143,8 +144,8 @@ def create_invalid_data_str(invalid_data):
     return err_str_data
 
 
-def make_iterable(a, ignore_str=True):
-    """ Convert noniterable type to singelton in list
+def make_iterable(a: Any, ignore_str: bool = True):
+    """ Convert noniterable type to singleton in list
 
     Args:
         a (T | Iterable[T]):

docs/_rtd/development.md

@@ -43,7 +43,7 @@ Miniforge contains conda with native Apple Silicon support. There are a few inst
 
 Now that Anaconda is installed, you can now create a `conda` environment. 
 
-To do so, on your command line, type `conda create -n <my_env> python=3.6`, where `<my_env>` is a name you set. Our codebase only supports Python 3.6, so please do not change the `python=3.6` flag when creating your environment. 
+To do so, on your command line, type `conda create -n <my_env> python=3.7`, where `<my_env>` is a name you set. Our codebase only supports Python 3.7, so please do not change the `python=3.7` flag when creating your environment. 
 
 Say yes to any prompts and your `conda` environment will be created! 
 

docs/conf.py

@@ -141,7 +141,7 @@
 # intersphinx mapping, for when there is a cross-reference that has no matching target
 # in the current documentation
 intersphinx_mapping = {
-    'python': ('https://docs.python.org/3.6', None),
+    'python': ('https://docs.python.org/3.7', None),
     'numpy': ('https://numpy.org/doc/stable', None),
     'matplotlib': ('https://matplotlib.org/3.2.1', None),
     'xarray': ('https://xarray.pydata.org/en/stable', None),

requirements-test.txt

@@ -1,10 +1,10 @@
-attrs>=20.3.0
-coveralls>=1.8.2,<2.0.0
-pytest<6.0.0
+attrs>=21.4.0
+coveralls>=1.11.1,<2.0.0
+pytest>=7.1.2,<8.0.0
 pytest-cases>=3.6.0,<4
 pytest-cov<3.0.0
 pytest-mock<4.0.0
 pytest-pycodestyle<3.0.0
-pytest-asyncio>=0.15.1
-six>=1.13.0
-testbook>=0.2.3,<1.0.0
+pytest-asyncio>=0.18.1,<2.0.0
+six>=1.16.0,<2.00
+testbook>=0.4.2,<1.0.0

requirements.txt

@@ -1,22 +1,23 @@
 cryptography>=3.4.8,<4
 feather-format>=0.4.1,<1
 jupyter>=1.0.0,<2
-ipympl==0.7.0
+importlib-metadata>=4.11.4,<5.0
+ipympl==0.9.1
 jupyter_contrib_nbextensions>=0.5.1,<1
-jupyterlab>=3.1.5,<4
+jupyterlab>=3.4.3,<4
 jedi>=0.17.2,<0.18
-matplotlib>=2.2.2,<3
-numpy>=1.16.3,<2
+matplotlib>=3.5.2,<4
+numpy>=1.21.6,<2
 palettable>=3.3.0,<4
-pandas>=0.23.3,<1
-requests>=2.25.1,<3
+pandas>=1.3.5,<2
+requests>=2.27.1,<3
 scikit-image>=0.14.3,<=0.16.2
-scikit-learn>=0.19.1,<1
-scipy>=1.1.0,<2
-seaborn>=0.10.1,<1
-git+https://github.com/calico/spatial_lda.git@primary
-statsmodels>=0.11.1,<1
-tables>=3.6.1,<4
-umap-learn>=0.4.6,<1
-xarray>=0.12.3,<1
-tqdm>=4.54.1,<5
+scikit-learn>=0.24.2,<1
+scipy>=1.7.3,<2
+seaborn>=0.11.2,<1
+spatial-lda>=0.1.3,<1
+statsmodels>=0.13.2,<1
+tables>=3.7.0,<4
+umap-learn>=0.5.3,<1
+xarray>=0.17.0,<1
+tqdm>=4.64.0,<5

setup.py

@@ -1,12 +1,17 @@
-from os import path
+from os import path, pardir
 from setuptools import setup, find_packages
 
-VERSION = '0.2.10'
+VERSION = '0.3.00'
+
+PKG_FOLDER = path.abspath(path.join(__file__, pardir))
 
 # set a long description which is basically the README
 with open(path.join(path.abspath(path.dirname(__file__)), 'README.md')) as f:
     long_description = f.read()
 
+with open(path.join(PKG_FOLDER, 'requirements.txt')) as req_file:
+    requirements = req_file.read().splitlines()
+
 setup(
     name='ark-analysis',
     version=VERSION,
@@ -16,29 +21,7 @@
     author='Angelo Lab',
     url='https://github.com/angelolab/ark-analysis',
     download_url='https://github.com/angelolab/ark-analysis/archive/v{}.tar.gz'.format(VERSION),
-    install_requires=['cryptography>=3.4.8,<4',
-                      'feather_format>=0.4.1,<1',
-                      'ipympl>=0.7.0,<0.8.0',
-                      'jupyter>=1.0.0,<2',
-                      'jupyter_contrib_nbextensions>=0.5.1,<1',
-                      'jupyterlab>=3.1.5,<4',
-                      'matplotlib>=2.2.2,<3',
-                      'numpy>=1.16.3,<2',
-                      'palettable>=3.3.0,<4',
-                      'pandas>=0.23.3,<1',
-                      'requests>=2.25.1,<3',
-                      'scikit-image>=0.14.3,<=0.16.2',
-                      'scikit-learn>=0.19.1,<1',
-                      'scipy>=1.1.0,<2',
-                      'seaborn>=0.10.1,<1',
-                      'spatial-lda>=0.1.3,<1',
-                      'statsmodels>=0.11.1,<1',
-                      'umap-learn>=0.4.6,<1',
-                      'xarray>=0.12.3,<1',
-                      'tqdm>=4.54.1,<5'],
-    dependency_links=[
-        'git+https://github.com/calico/spatial_lda.git@primary',
-    ],
+    install_requires=requirements,
     extras_require={
         'tests': ['pytest',
                   'pytest-cov',
@@ -50,5 +33,5 @@
     classifiers=['License :: OSI Approved :: Apache Software License',
                  'Development Status :: 4 - Beta',
                  'Programming Language :: Python :: 3',
-                 'Programming Language :: Python :: 3.6']
+                 'Programming Language :: Python :: 3.7']
 )

start_docker.sh

@@ -51,7 +51,7 @@ if [ ! -z "$external" ]
       -p $PORT:$PORT \
       -e JUPYTER_PORT=$PORT \
       -e JUPYTER_DIR=$JUPYTER_DIR \
-      -v "$PWD/ark:/usr/local/lib/python3.6/site-packages/ark" \
+      -v "$PWD/ark:/usr/local/lib/python3.7/site-packages/ark" \
       -v "$PWD/scripts:/scripts" \
       -v "$PWD/data:/data" \
       -v "$external:/data/external" \
@@ -68,7 +68,7 @@ if [ ! -z "$external" ]
       -p $PORT:$PORT \
       -e JUPYTER_PORT=$PORT \
       -e JUPYTER_DIR=$JUPYTER_DIR \
-      -v "$PWD/ark:/usr/local/lib/python3.6/site-packages/ark" \
+      -v "$PWD/ark:/usr/local/lib/python3.7/site-packages/ark" \
       -v "$PWD/scripts:/scripts" \
       -v "$PWD/data:/data" \
       -v "$PWD/ark/phenotyping/create_pixel_som.R:/create_pixel_som.R" \