Merge pull request #95 from rochefort-lab/rel_0.6.2

REL: Release version 0.6.2

.travis.yml

@@ -13,6 +13,8 @@ cache:
   directories:
     # Cache files downloaded by pip
     - $HOME/.cache/pip
+    # Cache our miniconda download.
+    - $HOME/Downloads
 
 ###############################################################################
 # version numbers
@@ -31,30 +33,33 @@ python:
 # environment variables
 env:
   - TEST_NOTEBOOKS="false"
-    USE_OLDEST_DEPENDENCIES="false"
+    USE_OLDEST_DEPS="false"
   - TEST_NOTEBOOKS="false"
-    USE_OLDEST_DEPENDENCIES="true"
+    USE_OLDEST_DEPS="true"
   - TEST_NOTEBOOKS="true"
-    USE_OLDEST_DEPENDENCIES="false"
+    USE_OLDEST_DEPS="false"
   - TEST_NOTEBOOKS="true"
-    USE_OLDEST_DEPENDENCIES="true"
+    USE_OLDEST_DEPS="true"
 
 matrix:
   exclude:
     # Currently, SIMA cannot be installed on Python 3.7
     - python: "3.7"
-      env: TEST_NOTEBOOKS="true" USE_OLDEST_DEPENDENCIES="false"
+      env: TEST_NOTEBOOKS="true" USE_OLDEST_DEPS="false"
     - python: "3.7"
-      env: TEST_NOTEBOOKS="true" USE_OLDEST_DEPENDENCIES="true"
+      env: TEST_NOTEBOOKS="true" USE_OLDEST_DEPS="true"
     # Currently, can't use our conda min numpy/scipy version detector on Travis
     # with weird Python 3.7
     - python: "3.7"
-      env: TEST_NOTEBOOKS="false" USE_OLDEST_DEPENDENCIES="true"
+      env: TEST_NOTEBOOKS="false" USE_OLDEST_DEPS="true"
   allow_failures:
-    - env: TEST_NOTEBOOKS="true" USE_OLDEST_DEPENDENCIES="true"
+    - env: TEST_NOTEBOOKS="true" USE_OLDEST_DEPS="true"
     # Currently, 'SIMA example.ipynb' is failing with Python 2.7.
     - python: "2.7"
-      env: TEST_NOTEBOOKS="true" USE_OLDEST_DEPENDENCIES="false"
+      env: TEST_NOTEBOOKS="true" USE_OLDEST_DEPS="false"
+  # Mark as failure as soon as a required job fails. Otherwise, mark as success
+  # as soon the only remaining jobs are allowed to fail.
+  fast_finish: true
 
 ###############################################################################
 # Setup the environment before installing
@@ -68,11 +73,11 @@ before_install:
   # Check which versions of numpy and scipy we are using, then remove these
   # lines from requirements.txt
   - if [ -f requirements.txt ]; then
-      NUMPY_REQUIREMENT="$(grep '^numpy\([<>=!]\|$\)' requirements.txt)";
+      NUMPY_REQUIREMENT="$(grep '^numpy\([!<>=~ ]\|$\)' requirements.txt)";
       echo "NumPy requirement is '$NUMPY_REQUIREMENT'";
-      SCIPY_REQUIREMENT="$(grep '^scipy\([<>=!]\|$\)' requirements.txt)";
+      SCIPY_REQUIREMENT="$(grep '^scipy\([!<>=~ ]\|$\)' requirements.txt)";
       echo "SciPy requirement is '$SCIPY_REQUIREMENT'";
-      sed '/^\(num\|sci\)py\([<>=!]\|$\)/d' requirements.txt >
+      sed '/^\(num\|sci\)py\([!<>=~ ]\|$\)/d' requirements.txt >
         requirements.txt.tmp &&
         mv requirements.txt.tmp requirements.txt;
     fi;
@@ -88,20 +93,21 @@ before_install:
   # ---------------------------------------------------------------------------
   # If we want to run the tests using the oldest set of dependencies we
   # support, modify any *requirements*.txt files every '>=' becomes '=='.
-  - if [[ "$USE_OLDEST_DEPENDENCIES" == "true" ]]; then
+  # Undo swapping any requirements which say version>=, since they are for
+  # our environment markers.
+  - if [[ "$USE_OLDEST_DEPS" == "true" ]]; then
       for FILE in *requirements*.txt; do
           sed -e 's/>=/~=/g' $FILE > $FILE.tmp && mv $FILE.tmp $FILE;
+          sed -e 's/version\s*~=/version>=/g' $FILE > $FILE.tmp && mv $FILE.tmp $FILE;
       done;
     fi;
   # ---------------------------------------------------------------------------
   # The following is based on Minicoda's how-to Travis page
   # http://conda.pydata.org/docs/travis.html
   # ---------------------------------------------------------------------------
-  # Download miniconda. Only do this if the cached file isn't present.
+  # Download miniconda. No need to redownload if we already have the latest version cached.
   - mkdir -p $HOME/Downloads;
-    if [ ! -f $HOME/Downloads/miniconda.sh ]; then
-      travis_retry wget https://repo.continuum.io/miniconda/Miniconda-latest-Linux-x86_64.sh -O "$HOME/Downloads/miniconda.sh";
-    fi;
+    travis_retry wget -c https://repo.continuum.io/miniconda/Miniconda-latest-Linux-x86_64.sh -O "$HOME/Downloads/miniconda.sh";
   # Install miniconda to the home directory, if it isn't there already.
   - if [ ! -d "$HOME/miniconda/bin" ]; then
       if [ -d "$HOME/miniconda" ]; then rm -r "$HOME/miniconda"; fi;
@@ -127,15 +133,21 @@ before_install:
   # possible requirement when scipy is being installed. The version of numpy
   # we end up must still satisfy the original requirement.txt setting, and
   # be from around the time of the oldest supported scipy release.
-  - if [[ "$USE_OLDEST_DEPENDENCIES" == "true" ]]; then
+  - if [[ "$USE_OLDEST_DEPS" == "true" ]]; then
       if [[ "$SCIPY_REQUIREMENT" != "" ]]; then
-          SCIPY_REQUIREMENT="scipy==$(bash
-              ./continuous_integration/conda_min_version.sh
+          SCIPY_VERSION="$(bash
+              ./.ci/conda_min_version.sh
               "$SCIPY_REQUIREMENT" "$TRAVIS_PYTHON_VERSION")";
+          if [[ "$SCIPY_VERSION" != "" ]]; then
+            SCIPY_REQUIREMENT="scipy==$SCIPY_VERSION";
+          fi;
       elif [[ "$NUMPY_REQUIREMENT" != "" ]]; then
-          NUMPY_REQUIREMENT="numpy==$(bash
-              ./continuous_integration/conda_min_version.sh
+          NUMPY_VERSION="$(bash
+              ./.ci/conda_min_version.sh
               "$NUMPY_REQUIREMENT" "$TRAVIS_PYTHON_VERSION")";
+          if [[ "$NUMPY_VERSION" != "" ]]; then
+            NUMPY_REQUIREMENT="numpy==$NUMPY_VERSION";
+          fi;
       fi;
     fi;
   # Create the conda environment with pip, numpy and scipy installed (if they
@@ -152,7 +164,7 @@ before_install:
   #
   # This is because you have constrained the numpy version in requirements.txt
   # to a more recent set of values (e.g. numpy>=1.9.0) than the scipy
-  # constraint (e.g. scipy>=0.12.0). The USE_OLDEST_DEPENDENCIES code has
+  # constraint (e.g. scipy>=0.12.0). The USE_OLDEST_DEPS code has
   # looked up the oldest compatible version available on conda (scipy==0.12.0)
   # but there is no numpy version for this which matches your constraint.
   #
@@ -240,7 +252,7 @@ script:
     fi;
   # Test the notebooks
   - if [[ "$TEST_NOTEBOOKS" == "true" ]]; then
-      ./continuous_integration/test_notebooks.sh -i ./examples;
+      ./.ci/test_notebooks.sh -i ./examples;
     fi;
 
 ###############################################################################

CHANGELOG.rst

@@ -12,6 +12,31 @@ Categories for changes are: Added, Changed, Deprecated, Removed, Fixed,
 Security.
 
 
+Version `0.6.2 <https://github.com/rochefort-lab/fissa/tree/0.6.2>`__
+---------------------------------------------------------------------
+
+Release date: 2020-03-11.
+Full commit changelog
+`on github <https://github.com/rochefort-lab/fissa/compare/0.6.1...0.6.2>`__.
+
+Fixed
+~~~~~
+
+-   Specify a maximum version for tifffile dependency on Python <3.6, which
+    allows us to continue supporting Python 2.7 and 3.5, which otherwise
+    fail to import dependencies correctly.
+    (`#87 <https://github.com/rochefort-lab/fissa/pull/87>`__)
+-   Documentation fixes and updates.
+    (`#64 <https://github.com/rochefort-lab/fissa/pull/64>`__,
+    `#65 <https://github.com/rochefort-lab/fissa/pull/65>`__,
+    `#67 <https://github.com/rochefort-lab/fissa/pull/67>`__,
+    `#76 <https://github.com/rochefort-lab/fissa/pull/76>`__,
+    `#77 <https://github.com/rochefort-lab/fissa/pull/77>`__,
+    `#78 <https://github.com/rochefort-lab/fissa/pull/78>`__,
+    `#79 <https://github.com/rochefort-lab/fissa/pull/79>`__,
+    `#92 <https://github.com/rochefort-lab/fissa/pull/92>`__)
+
+
 Version `0.6.1 <https://github.com/rochefort-lab/fissa/tree/0.6.1>`__
 ---------------------------------------------------------------------
 

HOWTO_RELEASE.md

@@ -146,7 +146,7 @@ Follow the instructions in the [PyPI tutorial](https://packaging.python.org/tuto
 rm -rf dist
 python -m pip install --upgrade setuptools wheel
 python -m pip install --upgrade twine
-python setup.py sdist bdist_wheel
+python setup.py sdist bdist_wheel --universal
 ```
 
 ## 6. Test the submission

LICENSE

@@ -1,7 +1,7 @@
                     GNU GENERAL PUBLIC LICENSE
                        Version 3, 29 June 2007
 
- Copyright (C) 2007 Free Software Foundation, Inc. <http://fsf.org/>
+ Copyright (C) 2007 Free Software Foundation, Inc. <https://fsf.org/>
  Everyone is permitted to copy and distribute verbatim copies
  of this license document, but changing it is not allowed.
 
@@ -631,8 +631,8 @@ to attach them to the start of each source file to most effectively
 state the exclusion of warranty; and each file should have at least
 the "copyright" line and a pointer to where the full notice is found.
 
-    {one line to give the program's name and a brief idea of what it does.}
-    Copyright (C) {year}  {name of author}
+    <one line to give the program's name and a brief idea of what it does.>
+    Copyright (C) <year>  <name of author>
 
     This program is free software: you can redistribute it and/or modify
     it under the terms of the GNU General Public License as published by
@@ -645,14 +645,14 @@ the "copyright" line and a pointer to where the full notice is found.
     GNU General Public License for more details.
 
     You should have received a copy of the GNU General Public License
-    along with this program.  If not, see <http://www.gnu.org/licenses/>.
+    along with this program.  If not, see <https://www.gnu.org/licenses/>.
 
 Also add information on how to contact you by electronic and paper mail.
 
   If the program does terminal interaction, make it output a short
 notice like this when it starts in an interactive mode:
 
-    {project}  Copyright (C) {year}  {fullname}
+    <program>  Copyright (C) <year>  <name of author>
     This program comes with ABSOLUTELY NO WARRANTY; for details type `show w'.
     This is free software, and you are welcome to redistribute it
     under certain conditions; type `show c' for details.
@@ -664,11 +664,11 @@ might be different; for a GUI interface, you would use an "about box".
   You should also get your employer (if you work as a programmer) or school,
 if any, to sign a "copyright disclaimer" for the program, if necessary.
 For more information on this, and how to apply and follow the GNU GPL, see
-<http://www.gnu.org/licenses/>.
+<https://www.gnu.org/licenses/>.
 
   The GNU General Public License does not permit incorporating your program
 into proprietary programs.  If your program is a subroutine library, you
 may consider it more useful to permit linking proprietary applications with
 the library.  If this is what you want to do, use the GNU Lesser General
 Public License instead of this License.  But first, please read
-<http://www.gnu.org/philosophy/why-not-lgpl.html>.
+<https://www.gnu.org/licenses/why-not-lgpl.html>.

README.rst

@@ -1,4 +1,4 @@
-|Gitter| |Travis| |Documentation| |Codecov| |Coveralls|
+|Gitter| |PyPI badge| |Travis| |Documentation| |Codecov| |Coveralls|
 
 
 FISSA
@@ -12,7 +12,9 @@ importing files stored in other formats.
 
 For details of the algorithm, please see our `companion
 paper <https://www.doi.org/10.1038/s41598-018-21640-2>`__ published in
-Scientific Reports.
+Scientific Reports. For the code used to generate the simulated data
+in the companion paper, see the
+`SimCalc repository <https://github.com/rochefort-lab/SimCalc/>`__.
 
 FISSA is compatible with both Python 2.7 and Python 3.5+. Using Python 3
 is strongly encouraged, as Python 2 will no longer be `maintained
@@ -181,11 +183,18 @@ interactive python session with the ``exit()`` command, or CTRL+D.
 Folder Structure
 ----------------
 
-continuous_integration/
-~~~~~~~~~~~~~~~~~~~~~~~
+A clone of this repository will contain directories detailed below.
 
-Contains files necessary for deploying tests on continuous integration
-servers. Users should ignore this directory.
+docs/
+~~~~~
+
+Contains the source for the documentation, which is available online at
+`<https://fissa.readthedocs.io>`_.
+You can build a local copy of the documentation by running the command
+
+::
+
+    make -C docs html
 
 examples/
 ~~~~~~~~~
@@ -213,6 +222,12 @@ fissa/tests/
 Contains tests for the toolbox, which are run to ensure it will work as
 expected.
 
+.ci/
+~~~~
+
+Contains files necessary for deploying tests on continuous integration
+servers. Users should ignore this directory.
+
 Citing FISSA
 ------------
 
@@ -223,7 +238,7 @@ S. W. Keemink, S. C. Lowe, J. M. P. Pakan, E. Dylda, M. C. W. van
 Rossum, and N. L. Rochefort. FISSA: A neuropil decontamination toolbox
 for calcium imaging signals, *Scientific Reports*, **8**\ (1):3493,
 2018.
-`DOI:10.1038/s41598-018-21640-2 <https://www.doi.org/10.1038/s41598-018-21640-2>`__.
+`doi: 10.1038/s41598-018-21640-2 <https://www.doi.org/10.1038/s41598-018-21640-2>`__.
 
 For your convenience, the FISSA package ships with a copy of this
 citation in bibtex format, available at
@@ -238,7 +253,7 @@ reserved.
 
 This program is free software; you can redistribute it and/or modify it
 under the terms of the GNU General Public License as published by the
-Free Software Foundation; either version 2 of the License, or (at your
+Free Software Foundation; either version 3 of the License, or (at your
 option) any later version.
 
 This program is distributed in the hope that it will be useful, but
@@ -252,6 +267,9 @@ with this program. If not, see http://www.gnu.org/licenses/.
 .. |Gitter| image:: https://badges.gitter.im/Join%20Chat.svg
    :target: https://gitter.im/rochefort-lab/fissa
    :alt: Join the FISSA chat
+.. |PyPI badge| image:: https://badge.fury.io/py/fissa.svg
+   :target: https://badge.fury.io/py/fissa
+   :alt: Latest PyPI release
 .. |Travis| image:: https://travis-ci.org/rochefort-lab/fissa.svg?branch=master
    :target: https://travis-ci.org/rochefort-lab/fissa
    :alt: Travis Build Status

citation.bib

@@ -5,7 +5,7 @@ @article{fissa
         and Dylda, Evelyn
         and van Rossum, Mark C. W.
         and Rochefort, Nathalie L.},
-    title={{FISSA}: A neuropil decontamination toolbox for calcium imaging signals},
+    title={{FISSA}: {A} neuropil decontamination toolbox for calcium imaging signals},
     journal={Scientific Reports},
     year={2018},
     volume={8},

docs/conf.py

@@ -12,20 +12,22 @@
 # add these directories to sys.path here. If the directory is relative to the
 # documentation root, use os.path.abspath to make it absolute, like shown here.
 #
+import datetime
 import os
 import sys
 sys.path.insert(0, os.path.abspath('.'))
 sys.path.insert(0, os.path.abspath('../'))
 
-from fissa import __meta__ as meta
+
+from fissa import __meta__ as meta  # noqa: E402
 
 
 # -- Project information -----------------------------------------------------
 
-import datetime
 now = datetime.datetime.now()
 
 project = meta.name.upper()
+project_path = meta.path
 author = meta.author
 copyright = '{}, {}'.format(now.year, author)
 
@@ -40,7 +42,7 @@
 
 def run_apidoc(_):
     ignore_paths = [
-        os.path.join('..', project.lower(), 'tests'),
+        os.path.join('..', project_path, 'tests'),
     ]
 
     argv = [
@@ -49,7 +51,7 @@ def run_apidoc(_):
         "--separate",  # Put each module file in its own page
         "--module-first",  # Put module documentation before submodule
         "-o", "source/packages",  # Output path
-        os.path.join("..", project.lower()),
+        os.path.join("..", project_path),
     ] + ignore_paths
 
     try:
@@ -62,13 +64,16 @@ def run_apidoc(_):
         argv.insert(0, apidoc.__file__)
         apidoc.main(argv)
 
+
 def retitle_modules(_):
     pth = 'source/packages/modules.rst'
     lines = open(pth).read().splitlines()
-    lines[0] = 'API'
-    lines[1] = '==='
+    # Overwrite the junk in the first two lines with a better title
+    lines[0] = 'API Reference'
+    lines[1] = '============='
     open(pth, 'w').write('\n'.join(lines))
 
+
 def setup(app):
     app.connect('builder-inited', run_apidoc)
     app.connect('builder-inited', retitle_modules)

fissa/__meta__.py

@@ -1,6 +1,6 @@
 name = 'fissa'
 path = name
-version = '0.6.1'
+version = '0.6.2'
 author = "Sander Keemink & Scott Lowe"
 author_email = "swkeemink@scimail.eu"
 description = "A Python Library estimating somatic signals in 2-photon data"