Patch v0.13.2 (#191)

* Enable code analysis by GitHub's CodeQL (#186)

* examples: fix rendering of RST code-blocks in notebooks (#179) (#184)

* Fix call to pipwin executable during PyPI installation (#187)

* `snlls`: Fix violation of boundaries due to float-point round-off errors  (#188)

* docs: fix automated example plots in the models reference (#190)

* VERSION: bump to v0.13.2

* Implement automated PyPI and Anaconda build and publish workflow (#185)

* Update CHANGELOG for v0.13.2

.github/actions/conda_build_publish_package/Dockerfile

@@ -0,0 +1,11 @@
+FROM continuumio/miniconda3:4.7.10
+
+LABEL "repository"="https://github.com/m0nhawk/conda-package-publish-action"
+LABEL "maintainer"="Andrew Prokhorenkov <andrew.prokhorenkov@gmail.com>"
+
+RUN conda install -y anaconda-client conda-build
+
+
+COPY entrypoint.sh /entrypoint.sh
+RUN chmod +x /entrypoint.sh
+ENTRYPOINT ["/entrypoint.sh"]

.github/actions/conda_build_publish_package/README.md

@@ -0,0 +1,63 @@
+# Build and Publish Anaconda Package
+
+A Github Action to publish your software package to an Anaconda repository.
+
+### Example workflow to publish to conda every time you make a new release
+
+```yaml
+name: publish_conda
+
+on:
+  release:
+    types: [published]
+
+jobs:
+  publish:
+    runs-on: ubuntu-latest
+    steps:
+    - uses: actions/checkout@v1
+    - name: publish-to-conda
+      uses: maxibor/conda-package-publish-action@v1.1
+      with:
+        subDir: 'conda'
+        AnacondaToken: ${{ secrets.ANACONDA_TOKEN }}
+        platforms: 'win-64 osx-64 linux-64'
+        python: '3.6 3.8'
+```
+
+### Example project structure
+
+```
+.
+├── LICENSE
+├── README.md
+├── myproject
+│   ├── __init__.py
+│   └── myproject.py
+├── conda
+│   ├── build.sh
+│   └── meta.yaml
+├── .github
+│   └── workflows
+│       └── publish_conda.yml
+├── .gitignore
+```
+### Inputs
+
+The action takes the following 
+
+- `AnacondaToken` - Anaconda access Token (see below)
+
+- `subDir` - (Optional) Sub-directory with conda recipe. Default: `.`
+
+- `platforms` - (Optional) Platforms to build and publish. Default: `win-64 osx-64 linux-64`.
+
+- `python` - (Optional) Python versions to build and publish. Default: `3.8`.
+
+### ANACONDA_TOKEN
+
+1. Get an Anaconda token (with read and write API access) at `anaconda.org/USERNAME/settings/access` 
+2. Add it to the Secrets of the Github repository as `ANACONDA_TOKEN`
+
+### Build Channels
+By Default, this Github Action will search for conda build dependancies (on top of the standard channels) in `conda-forge` and `bioconda`

.github/actions/conda_build_publish_package/action.yml

@@ -0,0 +1,21 @@
+name: 'Publish Conda package to Anaconda.org'
+description: 'Build and Publish conda package to Anaconda'
+author: 'Andrew Prokhorenkov, modified by Maxime Borry, modified by Luis Fabregas'
+branding:
+  icon: 'package'  
+  color: 'purple'
+inputs: 
+  subDir:
+    description: 'Sub-directory with conda recipe'
+    default: '.'
+  AnacondaToken:
+    description: 'Anaconda access Token'
+  platforms:
+    description: 'Platforms to build and publish [osx linux win]'
+    default: 'win-64 osx-64 linux-64'
+  python:
+    description: 'Python version to build and publish'
+    default: '3.8'
+runs:
+  using: 'docker'
+  image: 'Dockerfile'

.github/actions/conda_build_publish_package/entrypoint.sh

@@ -0,0 +1,50 @@
+#!/bin/bash
+
+set -ex
+set -o pipefail
+
+go_to_build_dir() {
+    if [ ! -z $INPUT_SUBDIR ]; then
+        cd $INPUT_SUBDIR
+    fi
+}
+
+check_if_meta_yaml_file_exists() {
+    if [ ! -f meta.yaml ]; then
+        echo "meta.yaml must exist in the directory that is being packaged and published."
+        exit 1
+    fi
+}
+
+build_package(){
+
+    IFS=' ' read -ra PYTHON <<< "$INPUT_PYTHON"
+    IFS=' ' read -ra PLATFORMS <<< "$INPUT_PLATFORMS"
+
+    for python in "${PYTHON[@]}"; do 
+        conda build -c conda-forge -c bioconda --output-folder . --python $python . 
+    done
+    for platform in "${PLATFORMS[@]}"; do 
+        for filename in /$platform/*.tar.bz2; do
+            conda convert -p $platform linux-64/*.tar.bz2
+        done 
+    done
+}
+
+upload_package(){
+
+    IFS=' ' read -ra PLATFORMS <<< "$INPUT_PLATFORMS"
+
+    export ANACONDA_API_TOKEN=$INPUT_ANACONDATOKEN
+
+    for platform in "${PLATFORMS[@]}"; do 
+        for filename in ./"$platform"/*.tar.bz2; do
+            anaconda upload $filename
+        done
+    done 
+}
+
+go_to_build_dir
+check_if_meta_yaml_file_exists
+build_package
+upload_package

.github/workflows/codeql-analysis.yml

@@ -0,0 +1,57 @@
+name: "CodeQL"
+
+on:
+  push:
+    branches: [ main, release/v0.13.0 ]
+  pull_request:
+    # The branches below must be a subset of the branches above
+    branches: [ main ]
+  schedule:
+    - cron: '33 11 * * 0'
+
+jobs:
+  analyze:
+    name: Analyze
+    runs-on: ubuntu-latest
+    permissions:
+      actions: read
+      contents: read
+      security-events: write
+
+    strategy:
+      fail-fast: false
+      matrix:
+        language: [ 'python' ]
+
+    steps:
+    - name: Checkout repository
+      uses: actions/checkout@v2
+
+    # Initializes the CodeQL tools for scanning.
+    - name: Initialize CodeQL
+      uses: github/codeql-action/init@v1
+      with:
+        languages: ${{ matrix.language }}
+        # If you wish to specify custom queries, you can do so here or in a config file.
+        # By default, queries listed here will override any specified in a config file.
+        # Prefix the list here with "+" to use these queries and those in the config file.
+        # queries: ./path/to/local/query, your-org/your-repo/queries@main
+
+    # Autobuild attempts to build any compiled languages  (C/C++, C#, or Java).
+    # If this step fails, then you should remove it and run the build manually (see below)
+    - name: Autobuild
+      uses: github/codeql-action/autobuild@v1
+
+    # ℹ️ Command-line programs to run using the OS shell.
+    # 📚 https://git.io/JvXDl
+
+    # ✏️ If the Autobuild fails above, remove it and uncomment the following three lines
+    #    and modify them (or add more) to build your code if your project
+    #    uses a compiled language
+
+    #- run: |
+    #   make bootstrap
+    #   make release
+
+    - name: Perform CodeQL Analysis
+      uses: github/codeql-action/analyze@v1

.github/workflows/package_upload.yml

@@ -0,0 +1,57 @@
+name: Build & Upload Python Package
+
+on: 
+  release:
+    types: [published]
+
+jobs:
+
+  pypi-build-n-publish:
+    runs-on: ubuntu-latest
+    steps:
+    - name: Checkout
+      uses: actions/checkout@v1
+    - name: Set up Python 3.8
+      uses: actions/setup-python@v1
+      with:
+        python-version: 3.8
+    - name: Install dependencies
+      run: |
+          apt-get install python3-pip -y
+          python -m pip install setuptools --user
+          python -m pip install build --user
+          python -m pip install twine --user
+          python -m pip install conda --user
+    - name: PyPI - Build and publish
+      run: |
+          python setup.py sdist
+          python -m twine upload dist/*
+    - name: Publish distribution to PyPI
+      uses: pypa/gh-action-pypi-publish@master
+      with:
+        password: ${{ secrets.PYPI_API_TOKEN  }}
+
+  conda-build-n-publish:
+    runs-on: ubuntu-latest
+    steps:
+    - name: Checkout
+      uses: actions/checkout@v1
+    - name: Set up Python 3.8
+      uses: actions/setup-python@v1
+      with:
+        python-version: 3.8
+    - name: Get DeerLab version
+      run: echo "DEERLAB_VERSION=$(cat VERSION)" >> $GITHUB_ENV
+    - name: Update version in Conda metadata 
+      uses: jacobtomlinson/gha-find-replace@master
+      with:
+        find: "VERSION"
+        replace: ${{env.DEERLAB_VERSION}}
+        include: "conda.recipe/meta.yaml" 
+    - name: Build & Publish to Anaconda
+      uses: ./.github/actions/conda_build_publish_package
+      with:
+        subdir: 'conda.recipe'
+        anacondatoken: ${{ secrets.ANACONDA_TOKEN }}
+        platforms: 'osx-64 linux-32 linux-64 win-32 win-64'
+        python: '3.6 3.7 3.8 3.9'

CHANGELOG.md

@@ -1,4 +1,15 @@
 
+Release v0.13.2 - July 2021
+---------------------------------
+
+#### Overall changes
+
+- Fixed an error appearing during installation in Windows systems. If during installation a  ``python`` executable alias was not created, the call to the ``pipwin`` manager returned an error and the installation failed to download and install Numpy, SciPy and cvxopt. ([#187](https://github.com/JeschkeLab/DeerLab/pull/187)).
+- Fixed the rendering of certain code-blocks in the documentation examples which were appearing as plain text ([#179](https://github.com/JeschkeLab/DeerLab/issues/179), [#184](https://github.com/JeschkeLab/DeerLab/pull/184)). 
+- Fixed the execution and rendering of the model examples in the documentation ([#189](https://github.com/JeschkeLab/DeerLab/issues/189), [#190](https://github.com/JeschkeLab/DeerLab/pull/190)). 
+- Fixed a bug in ``snlls`` where one of the linear least-squares solvers can return results that violate the boundary conditions due to float-point round-off errors ([#177](https://github.com/JeschkeLab/DeerLab/issues/177), [#188](https://github.com/JeschkeLab/DeerLab/pull/188)). 
+
+
 Release v0.13.1 - May 2021
 ---------------------------------
 

VERSION

@@ -1 +1 @@
-v0.13.1
+v0.13.2

conda.recipe/build.sh

@@ -0,0 +1 @@
+$PYTHON setup.py install     # Python command to install the script.

conda.recipe/meta.yaml

@@ -1,11 +1,9 @@
-{% set version = "v0.13.0" %}
-
 package:
   name: deerlab
-  version: {{ version }}
+  version: VERSION
 
 source:
-  git_rev: {{ version }}
+  git_rev: VERSION
   git_url: https://github.com/JeschkeLab/DeerLab.git
 
 requirements:

deerlab/dd_models.py

@@ -59,8 +59,7 @@ def docstr_example(fcnstr):
     import numpy as np 
     model = dl.{fcnstr}
     r = np.linspace(2,5,400)
-    info = model() 
-    par0 = info['Start']
+    par0 = model.start
     P = model(r,par0)
     plt.figure(figsize=[6,3])
     plt.plot(r,P)

deerlab/snlls.py

@@ -293,6 +293,9 @@ def snlls(y, Amodel, par0, lb=None, ub=None, lbl=None, ubl=None, nnlsSolver='cvx
         elif nnlsSolver == 'cvx':
             linSolver = lambda AtA, Aty: cvxnnls(AtA, Aty, tol=lin_tol, maxiter=lin_maxiter)
         parseResult = lambda result: result
+
+    # Ensure correct formatting and shield against float-point errors
+    validateResult = lambda result: np.maximum(lbl,np.minimum(ubl,np.atleast_1d(result)))
     # ----------------------------------------------------------
 
     # Containers for alpha-update checks
@@ -319,9 +322,9 @@ def linear_problem(A,optimize_alpha,alpha):
 
         # Solve the linear least-squares problem
         result = linSolver(AtA, Aty)
-        linfit = parseResult(result)
-        linfit = np.atleast_1d(linfit)
-        
+        result = parseResult(result)
+        linfit = validateResult(result)
+
         return linfit, alpha
     #===========================================================================
 
@@ -566,4 +569,3 @@ def _plot(subsets,y,yfit,show):
         plt.close()
     return fig
 # ===========================================================================================
-

deerlab/utils/utils.py

@@ -409,7 +409,7 @@ def Jacobian(fcn, x0, lb, ub):
 
     """
     J = opt._numdiff.approx_derivative(fcn,x0,method='2-point',bounds=(lb,ub))
-    J = np.atleast_2d(J)
+    J = np.atleast_2d(J) 
     return J
 #===============================================================================
 

examples/basic/ex_bootstrapping.py

@@ -11,12 +11,12 @@
 import deerlab as dl
 
 # %% [markdown]
-# Uncomment and use the following lines if you have experimental data:
-#
-# t,Vexp = dl.deerload('my\path\4pdeer_data.DTA')
-# Vexp = dl.correctphase(Vexp)
-# t = dl.correctzerotime(Vexp,t)
-#
+# Uncomment and use the following lines if you have experimental data::
+# 
+#   t,Vexp = dl.deerload('my\path\4pdeer_data.DTA')
+#   Vexp = dl.correctphase(Vexp)
+#   t = dl.correctzerotime(Vexp,t)
+# 
 
 # %% [markdown]
 # In this example we will use simulated data instead:

examples/basic/ex_fitting_4pdeer.py

@@ -15,12 +15,12 @@
 # Load and pre-process data
 # ---------------------------
 #
-# Uncomment and use the following lines if you have experimental data:
-#
-# t, Vexp = dl.deerload('my\path\4pdeer_data.DTA')
-# Vexp = dl.correctphase(Vexp)
-# t = dl.correctzerotime(Vexp,t)
-#
+# Uncomment and use the following lines if you have experimental data::
+# 
+#   t, Vexp = dl.deerload('my\path\4pdeer_data.DTA')
+#   Vexp = dl.correctphase(Vexp)
+#   t = dl.correctzerotime(Vexp,t)
+# 
 # In this example we will use simulated data instead.
 
 # %% [markdown]