Merge pull request #216 from kutaslab/dev

for release 0.5.2

.github/ISSUE_TEMPLATE/bug_report.md

@@ -0,0 +1,121 @@
+---
+name: Bug report
+about: Create a report to help us improve
+title: ''
+labels: ''
+assignees: ''
+
+---
+
+Thank you for helping to improve fitgrid.
+
+## Before you submit an issue please check your fitgrid installation.
+
+Problems are unavoidable when fitgrid is installed with incompatible or missing
+Python or R packages.
+
+Please try to replicate the issue after first using mamba or conda to install the latest fitgrid [stable version](https://kutaslab.github.io/fitgrid/installation.html#fitgrid-stable-release) into a newly created conda virtual environment.
+
+If the problem persists, please try to replicate the issue after installing the latest [pre-release version](https://kutaslab.github.io/fitgrid/installation.html#fitgrid-development-version) into a newly created conda virtual environment.
+
+**Warning: `pip install fitgrid` is officially not supported.**
+
+
+## Please provide the following information
+
+### 1. Description
+A clear and concise description of what the problem is, specifically:
+- What you expected to happen and what actually happened.
+- Anything you tried to solve the issue.
+
+### 2. Minimal reproducible example
+These are the shortest steps that reconstruct the problem.
+- The **exact** character-for-character command(s) you ran to to install fitgrid, copy-paste is best.
+- A Python code snippet or shell commands, the shorter the better, that runs and exhibits the issue.
+
+### 3. Conda environment
+Activate the conda environment that has fitgrid installed, run the following command in a terminal window, and upload the `fitgrid_issue.txt` file as an attachment with your issue.
+```
+conda list --explicit > fitgrid_issue.txt
+```
+
+### 4. System information
+Please provide the specifics about your computer hardware architecture and
+operating system version. For example:
+
+- Linux, in a terminal window
+
+```
+	$ uname -mprsv
+	Linux 3.10.0-957.21.3.el7.x86_64 #1 SMP Tue Jun 18 16:35:19 UTC 2019 x86_64 x86_64
+	
+	$ cat /etc/*-release
+	CentOS Linux release 7.3.1611 (Core) 
+	NAME="CentOS Linux"
+	VERSION="7 (Core)"
+	ID="centos"
+	ID_LIKE="rhel fedora"
+	VERSION_ID="7"
+	PRETTY_NAME="CentOS Linux 7 (Core)"
+	ANSI_COLOR="0;31"
+	CPE_NAME="cpe:/o:centos:centos:7"
+	HOME_URL="https://www.centos.org/"
+	BUG_REPORT_URL="https://bugs.centos.org/"
+	
+	CENTOS_MANTISBT_PROJECT="CentOS-7"
+	CENTOS_MANTISBT_PROJECT_VERSION="7"
+	REDHAT_SUPPORT_PRODUCT="centos"
+	REDHAT_SUPPORT_PRODUCT_VERSION="7"
+	
+	CentOS Linux release 7.3.1611 (Core) 
+	CentOS Linux release 7.3.1611 (Core) 
+```
+
+
+- Mac OSX, in a terminal window
+
+```
+	$ uname -mprsv
+	Darwin 19.6.0 Darwin Kernel Version 19.6.0: Thu Jun 18 20:49:00 PDT 2020; root:xnu-6153.141.1~1/RELEASE_X86_64 x86_64 i386
+
+	$ sw_vers
+	ProductName:	Mac OS X
+	ProductVersion:	10.15.6
+	BuildVersion:	19G2021
+```
+
+
+- [TODO: not officially supported] Windows, in a Windows Command Window
+
+```
+	C:\Users\some_user> systeminfo
+
+	Host Name:                 DESKTOP-G57OVSM
+	OS Name:                   Microsoft Windows 10 Home
+	OS Version:                10.0.18362 N/A Build 18362
+	OS Manufacturer:           Microsoft Corporation
+	OS Configuration:          Standalone Workstation
+	OS Build Type:             Multiprocessor Free
+	Registered Owner:          some_user
+	Registered Organization:
+	Product ID:                00326-00840-79774-AAOEM
+	Original Install Date:     7/29/2019, 6:13:59 AM
+	System Boot Time:          9/9/2020, 9:07:46 AM
+	System Manufacturer:       System manufacturer
+	System Model:              System Product Name
+	System Type:               x64-based PC
+	Processor(s):              1 Processor(s) Installed.
+    [01]: Intel64 Family 6 Model 158 Stepping 12 GenuineIntel ~3600 Mhz
+	BIOS Version:              American Megatrends Inc. 0606, 8/31/2018
+	Windows Directory:         C:\WINDOWS
+	System Directory:          C:\WINDOWS\system32
+	Boot Device:               \Device\HarddiskVolume2
+	System Locale:             en-us;English (United States)
+	Input Locale:              en-us;English (United States)
+	Time Zone:                 (UTC-08:00) Pacific Time (US & Canada)
+	Total Physical Memory:     16,305 MB
+	Available Physical Memory: 13,598 MB
+	Virtual Memory: Max Size:  18,737 MB
+	Virtual Memory: Available: 14,542 MB
+	Virtual Memory: In Use:    4,195 MB
+```

.github/workflows/fitgrid-cid.yml

@@ -119,21 +119,23 @@ jobs:
 
           # switch to mamba/boa and conda-forge
           conda config --add channels conda-forge
-          conda config --set channel_priority strict
-          conda install -n base -q conda-build conda-verify anaconda-client twine mamba boa
+
+          # revised mamba channel priority semantics, strict in 0.14 is flexible in 0.15
+          conda config --set channel_priority flexible  # should be default but enforce
+          conda install -n base -q conda-build conda-verify anaconda-client mamba boa
           echo "# ------------------------------------------------------------"
           conda info -a
           echo "# ------------------------------------------------------------"
           mamba info -a
 
       # ------------------------------------------------------------
       # 2. CI
-      - name: conda build --python=${{ env.PY_VER }} conda
+      - name: conda mambabuild --python=${{ env.PY_VER }} conda
         id: conda-bld
         env:
           OS: ${{ runner.os }}   # Linux, macOS
         run: |
-          # conda-forge added in setup w/ strict priority
+          # conda-forge added in setup
           conda mambabuild --python=$PY_VER -c ejolly conda
           # filename is last line when conda build is chatty
           tarball=$(conda build --python=$PY_VER conda --output | tail -1)
@@ -144,11 +146,12 @@ jobs:
           fi
           echo "conda build tarball" $tarball
           echo "::set-output name=conda-tarball::$tarball"
+          mamba search fitgrid -c $CONDA_BLD_PATH
 
       # create an env w/ local package
-      - name: conda create env_${{ env.PY_VER }} python=${{ env.PY_VER }} ${{ env.PACKAGE_NAME}} and black
+      - name: conda create env_${{ env.PY_VER }} python=${{ env.PY_VER }} ${{ env.PACKAGE_NAME}}
         run: |
-          mamba create -n env_$PY_VER python=$PY_VER $PACKAGE_NAME "blas=*=mkl*" -c local -c ejolly
+          mamba create -n env_$PY_VER python=$PY_VER $PACKAGE_NAME "blas=*=mkl*" -c $CONDA_BLD_PATH -c ejolly
 
       - name: black, pytest, codecov
         run: |

.gitignore

@@ -1,3 +1,11 @@
+# built files
+docs/source/auto_gallery/*
+
+# Zenodo data downloads
+fitgrid/data/sub000*.feather
+fitgrid/data/sub000*.h5
+fitgrid/data/sub000*.pdh5
+
 # TODOs files
 *.todo
 

docs/Makefile

@@ -20,8 +20,10 @@ help:
 	@$(SPHINXBUILD) -M $@ "$(SOURCEDIR)" "$(BUILDDIR)" $(SPHINXOPTS) $(O)
 
 api-rst: 
-	ls source/api_docs
 	sphinx-apidoc -e -f -o source/api_docs ../fitgrid
+	awk 'BEGIN{printf(":orphan:\n\n")}{print}' source/api_docs/modules.rst > source/api_docs/modules.tmp
+	mv source/api_docs/modules.tmp source/api_docs/modules.rst
+	ls source/api_docs
 
 # just format .rst, don't run sphinx-gallery scripts
 html-noexec: api-rst

docs/source/about_fitgrid.rst

@@ -139,7 +139,8 @@ information criterion, model and error mean squares, and so forth. The
 results are returned as tidy Time x Channel dataframes for handy
 visualization and analysis in Python and data interchange across
 scientific computing platforms as illustrated in
-:ref:`workflow` and the :ref:`gallery`.
+:ref:`workflow` and the :ref:`gallery`. For examles of ``fitgrid``
+at work see [TroUrbKut2020]_ and [UrbachEtAl2020]_.
 
 ================================
 ``fitgrid`` design: How it works

docs/source/api.rst

@@ -16,10 +16,11 @@ Quick reference
 
    quick_reference
 
-
 =======
 Indexes
 =======
 
 * :ref:`Alphabetical Index <genindex>`
 * :ref:`Module Index <modindex>`
+
+

docs/source/conf.py

@@ -63,6 +63,7 @@
 
 napoleon_google_docstring = False
 napoleon_use_param = False
+napoleon_use_keyword = False
 napoleon_use_ivar = True
 
 # ------------------------------------------------------------
@@ -164,13 +165,16 @@ def __call__(self, *args, **kwargs):
 # The name of the Pygments (syntax highlighting) style to use.
 pygments_style = 'sphinx'
 
+# -- autodoc --------------------------------------------------
+autodoc_default_options = {'show_inheritance': True}
 
 # -- Options for HTML output -------------------------------------------------
 
 # The theme to use for HTML and HTML Help pages.  See the documentation for
 # a list of builtin themes.
 #
 html_theme = 'sphinx_rtd_theme'
+# html_theme = 'bootstrap'
 html_copy_source = False
 html_show_sourcelink = False
 html_show_sphinx = False