Merge pull request #257 from jellis18/master

Updating github actions and requirements. Thanks @jellis18 and @Hazboun6! I think it's time to press the green button on this one. We can clean up import warnings later.

.github/workflows/ci_test.yml

@@ -1,52 +1,132 @@
-name: CI-Tests
+name: enterprise CI targets
 
 on:
   push:
-#    branches:
-#    - master
+    branches: [ master ]
   pull_request:
+    branches: [ master ]
+  release: 
+    types:
+      - published
+
 
 jobs:
-  lint:
-    runs-on: ubuntu-latest
-    steps:
-      - uses: actions/checkout@v2
-      - uses: actions/setup-python@v2
-      - uses: psf/black@stable
-  build:
-    runs-on: ubuntu-latest
+  tests:
+    runs-on: ${{ matrix.os }}
     strategy:
       fail-fast: false
       matrix:
+        os: [ubuntu-latest, macos-latest]
         python-version: [3.6, 3.7, 3.8]
+
     steps:
-    - name: Checkout Repository
+    - name: Checkout repository
       uses: actions/checkout@v2
     - name: Set up Python ${{ matrix.python-version }}
       uses: actions/setup-python@v2
       with:
         python-version: ${{ matrix.python-version }}
-    - name: Pre-install
+    - name: Install non-python dependencies on mac
+      if: runner.os == 'macOS'
+      run: |
+        brew unlink gcc && brew link gcc
+        brew install automake suite-sparse
+        curl -sSL https://raw.githubusercontent.com/vallis/libstempo/master/install_tempo2.sh | sh
+    - name: Install non-python dependencies on linux
+      if: runner.os == 'Linux'
       run: |
         sudo apt-get install libsuitesparse-dev
         curl -sSL https://raw.githubusercontent.com/vallis/libstempo/master/install_tempo2.sh | sh
-        python -m pip install --upgrade pip
-    - name: Install Dependencies
+    - name: Install dependencies and package
       run: |
-        cat requirements_dev.txt | xargs -n 1 -L 1 pip install
-        cat requirements.txt | xargs -n 1 -L 1 pip install
-        python setup.py install
+        python -m pip install --upgrade pip setuptools wheel
+        python -m pip install flake8 pytest black pytest-cov
+        python -m pip install numpy cython
+        python -m pip install -e .
     - name: Display Python, pip, setuptools, and all installed versions
       run: |
         python -c "import sys; print(f'Python {sys.version}')"
         python -c "import pip; print(f'pip {pip.__version__}')"
         python -c "import setuptools; print(f'setuptools {setuptools.__version__}')"
-        pip freeze
-    - name: Run Tests and Lint
-      run: |
-        pytest --cov-config=.coveragerc --cov=enterprise --cov-report=xml
-        make lint
+        python -m pip freeze
+    - name: Run lint
+      run: make lint
+    - name: Test with pytest
+      run: make test
     - name: Codecov
       uses: codecov/codecov-action@v1
+      #with:
+      #  fail_ci_if_error: true
+
+
+  build:
+    needs: [tests]
+    name: Build source distribution
+    runs-on: ubuntu-latest
+    if: github.event_name == 'release'
+
+    steps:
+    - uses: actions/checkout@v2
+    - name: Set up Python 
+      uses: actions/setup-python@v2
       with:
-        fail_ci_if_error: true
+        python-version: "3.7"
+    - name: Install non-python dependencies on linux
+      run: |
+        sudo apt-get install libsuitesparse-dev
+        curl -sSL https://raw.githubusercontent.com/vallis/libstempo/master/install_tempo2.sh | sh
+    - name: Build
+      run: |
+        python -m pip install --upgrade pip setuptools wheel
+        pip install numpy==1.16.3 cython
+        pip install -r requirements.txt
+        make dist
+    - name: Test the sdist
+      run: |
+        mkdir tmp  
+        cd tmp
+        python -m venv venv-sdist
+        venv-sdist/bin/python -m pip install --upgrade pip setuptools wheel
+        venv-sdist/bin/python -m pip install numpy cython
+        venv-sdist/bin/python -m pip install ../dist/enterprise*.tar.gz
+        venv-sdist/bin/python -c "import enterprise;print(enterprise.__version__)"
+    - name: Test the wheel
+      run: |
+        mkdir tmp2  
+        cd tmp2
+        python -m venv venv-wheel
+        venv-wheel/bin/python -m pip install --upgrade pip setuptools
+        venv-wheel/bin/python -m pip install numpy cython
+        venv-wheel/bin/python -m pip install ../dist/enterprise*.whl
+        venv-wheel/bin/python -c "import enterprise;print(enterprise.__version__)"
+    - uses: actions/upload-artifact@v2
+      with:
+        name: dist
+        path: dist/*
+
+
+  deploy:
+    needs: [tests, build]
+    runs-on: ubuntu-latest
+    if: github.event_name == 'release'
+    steps:
+    - uses: actions/checkout@v2
+    - name: Set up Python
+      uses: actions/setup-python@v2
+      with:
+        python-version: '3.7'
+    - name: Install dependencies
+      run: |
+        python -m pip install --upgrade pip
+        pip install setuptools wheel twine
+    - name: Download wheel/dist from build
+      uses: actions/download-artifact@v2
+      with:
+        name: dist
+        path: dist
+    - name: Build and publish
+      env:
+        TWINE_USERNAME: ${{ secrets.PYPI_USERNAME }}
+        TWINE_PASSWORD: ${{ secrets.PYPI_PASSWORD }}
+      run: |
+        twine upload dist/*

.isort.cfg

@@ -0,0 +1,6 @@
+[settings]
+include_trailing_comma=True
+indent='    '
+dedup_headings=True
+line_length=120
+multi_line_output=3

.pre-commit-config.yaml

@@ -9,3 +9,8 @@ repos:
     hooks:
     - id: flake8
       args: ["--config=.flake8"]
+- repo: https://github.com/timothycrosley/isort
+  rev: 5.6.1
+  hooks:
+    - id: isort
+

CONTRIBUTING.rst

@@ -72,14 +72,17 @@ Ready to contribute? Here's how to set up `enterprise` for local development.
    
     $ git pull upstream master
 
-4. Install your local copy into a virtualenv. Assuming you have virtualenvwrapper installed, this is how you set up your fork for local development::
+4. This is how you set up your fork for local development:
+
+    .. note:: 
+        You will need to have ``tempo`` and ``suitesparse`` installed before  
+        running the commands below. 
+
+ ::
 
-    $ mkvirtualenv enterprise
     $ cd enterprise/
-    $ pip install -r requirements_dev.txt
-    $ pip install -r requirements.txt
-    $ pip install libstempo --install-option="--with-tempo2=$TEMPO2"
-    $ python setup.py develop
+    $ make init
+    $ source .enterprise/bin/activate  
 
 5. Create a branch for local development::
 

Makefile

@@ -28,12 +28,14 @@ help:
 
 init:
 	@python3 -m venv .enterprise --prompt enterprise
-	@./.enterprise/bin/python3 -m pip install numpy
+	@./.enterprise/bin/python3 -m pip install -U pip setuptools wheel
+	@./.enterprise/bin/python3 -m pip install numpy cython
 	@./.enterprise/bin/python3 -m pip install -r requirements.txt -U
 	@./.enterprise/bin/python3 -m pip install -r requirements_dev.txt -U
-	@./.enterprise/bin/python3 -m pip install libstempo --install-option="--with-tempo2=$(TEMPO2)"
 	@./.enterprise/bin/python3 -m pre_commit install --install-hooks --overwrite
 	@./.enterprise/bin/python3 -m pip install -e .
+	@echo "run source .enterprise/bin/activate to activate environment"
+
 
 format:
 	black .
@@ -61,24 +63,20 @@ clean-test: ## remove test and coverage artifacts
 	rm -fr .tox/
 	rm -f .coverage
 	rm -fr htmlcov/
+	rm -rf coverage.xml
 
-test: ## run tests quickly with the default Python
-	pytest -v --full-trace --cov-config .coveragerc --cov=enterprise tests
-
-#test-all: ## run tests on every Python version with tox
-#	tox
-
-coverage: ## check code coverage quickly with the default Python
-	coverage run --source enterprise setup.py test
+COV_COVERAGE_PERCENT ?= 85
+test: lint ## run tests quickly with the default Python
+	pytest -v --durations=10 --full-trace --cov-report html --cov-report xml \
+		--cov-config .coveragerc --cov-fail-under=$(COV_COVERAGE_PERCENT) \
+		--cov=enterprise tests
 
-	coverage report -m
-	coverage html
+coverage: test ## check code coverage quickly with the default Python
 	$(BROWSER) htmlcov/index.html
 
-jupyter-docs:
+jupyter-docs: ## biuld jupyter notebook docs
 	jupyter nbconvert --template docs/nb-rst.tpl --to rst docs/_static/notebooks/*.ipynb --output-dir docs/
 	cp -r docs/_static/notebooks/img docs/
-	#jupyter nbconvert --template docs/nb-rst.tpl --to rst docs/_static/notebooks/tutorials/*.ipynb --output-dir docs/tutorials/
 
 docs: ## generate Sphinx HTML documentation, including API docs
 	rm -f docs/enterprise*.rst
@@ -92,14 +90,7 @@ docs: ## generate Sphinx HTML documentation, including API docs
 servedocs: docs ## compile the docs watching for changes
 	watchmedo shell-command -p '*.rst' -c '$(MAKE) -C docs html' -R -D .
 
-release: clean ## package and upload a release
-	python setup.py sdist upload
-	python setup.py bdist_wheel upload
-
 dist: clean ## builds source and wheel package
 	python setup.py sdist
 	python setup.py bdist_wheel
 	ls -l dist
-
-install: clean ## install the package to the active Python's site-packages
-	python setup.py install

enterprise/pulsar.py

@@ -6,8 +6,8 @@
 import logging
 import os
 
-import astropy.units as u
 import astropy.constants as const
+import astropy.units as u
 import numpy as np
 from ephem import Ecliptic, Equatorial
 
@@ -19,29 +19,28 @@
 except:
     import pickle
 
+logger = logging.getLogger(__name__)
+
 try:
     import libstempo as t2
 except ImportError:
-    print("Ooh, no libstempo?")
+    logger.warning("libstempo not installed. Will use PINT instead.")  # pragma: no cover
     t2 = None
 
 try:
     import pint
-    from pint.toa import TOAs
-    from pint.models import get_model_and_toas, TimingModel
+    from pint.models import TimingModel, get_model_and_toas
     from pint.residuals import Residuals as resids
+    from pint.toa import TOAs
 except ImportError:
-    print("Cannot import PINT? Meh...")
+    logger.warning("PINT not installed. Will use libstempo instead.")  # pragma: no cover
     pint = None
 
 
 if pint is None and t2 is None:
     err_msg = "Must have either PINT or libstempo timing package installed"
     raise ImportError(err_msg)
 
-# logging.basicConfig(format="%(levelname)s: %(name)s: %(message)s", level=logging.INFO)
-logger = logging.getLogger(__name__)
-
 
 def get_maxobs(timfile):
     """Utility function to return number of lines in tim file.
@@ -119,7 +118,7 @@ def sort_data(self):
         """Sort data by time."""
         if self._sort:
             self._isort = np.argsort(self._toas, kind="mergesort")
-            self._iisort = np.zeros(len(self._isort), dtype=np.int)
+            self._iisort = np.zeros(len(self._isort), dtype=int)
             for ii, p in enumerate(self._isort):
                 self._iisort[p] = ii
         else:
@@ -586,5 +585,5 @@ def Pulsar(*args, **kwargs):
             t2pulsar = t2.tempopulsar(relparfile, reltimfile, maxobs=maxobs, ephem=ephem, clk=clk)
             os.chdir(cwd)
             return Tempo2Pulsar(t2pulsar, sort=sort, drop_t2pulsar=drop_t2pulsar, planets=planets)
-    else:
-        print("Unknown arguments {}".format(args))
+
+    raise ValueError("Unknown arguments {}".format(args))

enterprise/signals/selections.py

@@ -2,7 +2,6 @@
 """Contains various selection functions to mask parameters by backend flags,
 time-intervals, etc."""
 
-from __future__ import absolute_import, division, print_function, unicode_literals
 
 import functools
 import inspect

enterprise/signals/signal_base.py

@@ -3,14 +3,13 @@
 Defines the signal base classes and metaclasses. All signals will then be
 derived from these base classes.
 """
-from __future__ import absolute_import, division, print_function, unicode_literals
-
 import collections
 
 try:
     from collections.abc import Sequence
 except:
     from collections import Sequence
+
 import itertools
 import logging
 
@@ -546,10 +545,11 @@ def _setpulsarcliques(self, slices, phis):
                         try:
                             self._cliques[slices[sc].start + phiind] = self._clcount
                             self._clcount = self._clcount + 1
-                        except:
-                            print(self._cliques.shape)
-                            print("phiind", phiind, len(phiind))
-                            print(slices)
+                        except Exception:  # pragma: no cover
+                            logger.exception("Exception raised in computing cliques")
+                            logger.info(self._cliques.shape)
+                            logger.info("phiind", phiind, len(phiind))
+                            logger.info(slices)
                             raise
 
     def get_phi(self, params, cliques=False):
@@ -684,7 +684,7 @@ def summary(self, include_params=True, to_stdout=False):
         summary += "Fixed params: {}\n".format(copcount)
         summary += "Number of pulsars: {}\n".format(len(self._signalcollections))
         if to_stdout:
-            print(summary)
+            logger.info(summary)
         else:
             return summary