Merge pull request #55 from drsmith48/drs-dev

drs-dev

.bumpversion.cfg

@@ -0,0 +1,15 @@
+[bumpversion]
+current_version = 0.2.0
+commit = True
+tag = True
+verbose = True
+list = True
+
+[bumpversion:file:fdp/__init__.py]
+search = __version__ = '{current_version}'
+replace = __version__ = '{new_version}'
+
+[bumpversion:file:docs/source/conf.py]
+search = version = '{current_version}'
+replace = version = '{new_version}'
+

.coveragerc

@@ -0,0 +1,18 @@
+[run]
+source = fdp
+branch = False
+
+[report]
+show_missing = True
+ignore_errors = True
+exclude_lines =
+    pragma: no cover
+    if self.debug:
+    if debug:
+    if self.verbose:
+    if verbose:
+    if VERBOSE:
+    if __name__ == .__main__.:
+
+[html]
+directory = htmlcov

.flake8

@@ -0,0 +1,8 @@
+[flake8]
+exclude = docs
+max-line-length = 79
+show-source = True
+statistics = True
+output-file = flake8.output.txt
+tee = True
+max-complexity = 10

.gitignore

@@ -3,14 +3,27 @@
 #
 
 *~
-*.pyc
-docs/build
+*.py[cod]
+__pycache__/
+*$py.class
+docs/build/
 *.ipynb
 .ipynb_checkpoints
 .spyderproject
 anaconda
 .DS_Store
 spyder_crash.log
+CHANGELOG.copy.txt
+
+# Unit test / coverage reports
+htmlcov/
+.tox/
+.coverage
+.coverage.*
+.cache
+nosetests.xml
+coverage.xml
+flake8.output.txt
 
 
 #

AUTHORS.txt

@@ -0,0 +1,18 @@
+Lead developers:
+    David R. Smith
+    Kevin Tritz
+    Howard Yuh
+Commits from authors:
+   277	David R. Smith
+    37	ktritz
+    22	dmkriete
+     2	hyyuh
+     1	Howard Yuh
+Commits from obsolete FDF repository:
+   261  David R. Smith
+    41  Kevin Tritz
+    17  ktritz
+    10  Howard Yuh
+     7  John Schmitt
+     4  hyyuh
+     2  jcschmitt

CHANGELOG.txt

@@ -0,0 +1,31 @@
+Release v0.2.0 -- 2017-04-19\n
+4abf46b tests
+6564d4c changed 'fdp_globals' to 'globals' throughout repo
+dea305b changed fdp_globals import
+ea12a72 tests
+54cb3a7 Merge branch 'drs-dev' of github.com:drsmith48/fdp into drs-dev
+74c271f tests
+ff08bd2 tests
+63ce140 tests
+af97cda testing for logbook.py and machine.py
+8fbaf30 pytest setup
+534f00a created new test directory and configured for pytest; run 'pytest' or 'make test'
+3f59f74 minor
+be1449c minor
+a8e38e3 fixed axis removal from multi-dim signals
+9400ca8 Merge branch 'master' into drs-dev
+8e2d471 Merge pull request #54 from drsmith48/plotpsirz
+33c025e debugging eq.plotrz.plot()
+7adfae2 bfield() method for equilibria
+ddd16a5 minor fixes
+ea8852b changed 'zero level' indices to floats
+09f779a changed iteritems to iter()
+7d32fd6 docs
+bab6bbc docs
+fa1a1fb docs
+17e9578 removed pushes from bumps in Makefile
+a06ac9b run 'authors' recipe prior to 'bump-*' recipes in Makefile
+\n
+Release v0.1.4 -- 2017-04-07
+
+a2842c8 added automatic CHANGELOG.txt updates with 'bump-*' recipes in Makefile

CONTRIBUTING.rst

@@ -0,0 +1,41 @@
+========================
+How to contribute
+========================
+
+* Github repository: https://github.com/Fusion-Data-Platform/fdp
+* Submit bugs and feature requests as Github issues: https://github.com/Fusion-Data-Platform/fdp/issues
+* Google group: https://groups.google.com/forum/#!forum/fusion-data-platform
+
+**Code**
+
+Thank you for your interest in the FDP project.  To contribute to the FDP code base, fork the repo at Github and submit pull requests with your contributions.  Read more:
+
+* https://guides.github.com/activities/forking/
+* https://help.github.com/articles/fork-a-repo/
+
+**Style**
+
+Please try to follow the `PEP8 style guide <https://www.python.org/dev/peps/pep-0008/>`_.  To scan for PEP8 conformance, run ``make lint`` in the top-level directory.
+
+**Makefile utilities**
+
+The top-level ``Makefile`` contains several utilities for generating docs, code style/quality reviews, and versioning:
+
+.. code-block:: shell
+
+    $ make help
+    help                 show this help message
+    docs                 build HTML and PDF documents
+    docs-html            build HTML documents
+    docs-pdf             build PDF documents
+    test                 run pytest in current Python environment
+    lint                 run flake8 for code quality review
+    autopep              run autopep8 to fix minor pep8 violations
+    authors              update AUTHORS.txt
+    bump-major           update AUTHORS and CHANGELOG; bump major version and tag
+    bump-minor           update AUTHORS and CHANGELOG; bump minor version and tag
+    bump-patch           update AUTHORS and CHANGELOG; bump patch version and tag
+    clean                remove all build, docs, and Python artifacts
+    clean-docs           remove docs/build
+    clean-pyc            remove Python file artifacts
+

LICENSE.rst → LICENSE.txt

@@ -1,7 +1,4 @@
-
-The MIT License (MIT)
-
-Copyright (c) 2015 John Schmitt, David R. Smith, Kevin Tritz, Howard Yuh
+Copyright (c) 2015-2017  David R. Smith, Kevin Tritz, Howard Yuh
 
 Permission is hereby granted, free of charge, to any person obtaining a copy
 of this software and associated documentation files (the "Software"), to deal

Makefile

@@ -1,7 +1,185 @@
-.PHONY: build-docs
+.DEFAULT_GOAL := help
 
-DOCDIR = docs
+today := $(shell date +%F)
 
-build-docs:
-	rm -rf $(DOCDIR)/build/html/
-	$(MAKE) -C $(DOCDIR) html
+nextmajorversion := $(shell bumpversion \
+  --no-commit --no-tag --dry-run --list major --allow-dirty | \
+  grep "^new_version=.*$$" | \
+  grep -o "[0-9]*\.[0-9]*\.[0-9]*$$")
+nextminorversion := $(shell bumpversion \
+  --no-commit --no-tag --dry-run --list minor --allow-dirty | \
+  grep "^new_version=.*$$" | \
+  grep -o "[0-9]*\.[0-9]*\.[0-9]*$$")
+nextpatchversion := $(shell bumpversion \
+  --no-commit --no-tag --dry-run --list patch --allow-dirty | \
+  grep "^new_version=.*$$" | \
+  grep -o "[0-9]*\.[0-9]*\.[0-9]*$$")
+
+define LEAD_AUTHORS
+Lead developers:
+    David R. Smith
+    Kevin Tritz
+    Howard Yuh
+endef
+export LEAD_AUTHORS
+
+
+define FDF_SHORTLOG
+Commits from obsolete FDF repository:
+   261  David R. Smith
+    41  Kevin Tritz
+    17  ktritz
+    10  Howard Yuh
+     7  John Schmitt
+     4  hyyuh
+     2  jcschmitt
+endef
+export FDF_SHORTLOG
+
+define PRINT_HELP_PYSCRIPT
+import re, sys
+for line in sys.stdin:
+	match = re.match(r'^([a-zA-Z_-]+):.*?## (.*)$$', line)
+	if match:
+		target, help = match.groups()
+		print("%-20s %s" % (target, help))
+endef
+export PRINT_HELP_PYSCRIPT
+
+
+define BROWSER_PYSCRIPT
+import os, webbrowser, sys
+try:
+	from urllib import pathname2url
+except:
+	from urllib.request import pathname2url
+
+webbrowser.open("file://" + pathname2url(os.path.abspath(sys.argv[1])))
+endef
+export BROWSER_PYSCRIPT
+BROWSER := python -c "$$BROWSER_PYSCRIPT"
+
+
+.PHONY: help
+help: ## show this help message
+	@python -c "$$PRINT_HELP_PYSCRIPT" < $(MAKEFILE_LIST)
+
+
+.PHONY: docs
+docs: docs-pdf docs-html ## build HTML and PDF documents
+
+
+.PHONY: docs-html
+docs-html: ## build HTML documents
+	$(MAKE) -C docs/ html
+	@$(BROWSER) docs/build/html/index.html
+
+
+.PHONY: docs-pdf
+docs-pdf: ## build PDF documents
+	$(MAKE) -C docs/ latexpdf
+
+
+.PHONY: outdated
+outdated:  # list outdated conda and pip packages
+	@echo "outdated conda packages"
+	@conda update --dry-run --all
+	@echo "outdated pip packages (may be managed by conda)"
+	@pip list --outdated
+
+
+.PHONY: test
+test: ## run pytest in current Python environment
+	pytest
+
+
+.PHONY: coverage
+coverage: ## check test coverage and show report in terminal
+	@rm -f .coverage
+	coverage run --module pytest
+	coverage report
+
+
+.PHONY: coverage-html
+coverage-html: coverage ## check test coverage and show report in browser
+	@rm -fr htmlcov/
+	@coverage html
+	@$(BROWSER) htmlcov/index.html
+
+
+.PHONY: lint
+lint:  ## run flake8 for code quality review
+	@rm -f flake8.output.txt
+	flake8 --exit-zero fdp/
+
+
+.PHONY: autopep
+autopep:  ## run autopep8 to fix minor pep8 violations
+	autopep8 --in-place -r fdp/
+	autopep8 --in-place -r test/
+
+
+.PHONY: authors
+authors:  ## update AUTHORS.txt
+	@echo "$$LEAD_AUTHORS" > AUTHORS.txt
+	@echo "Commits from authors:" >> AUTHORS.txt
+	@git shortlog -s -n >> AUTHORS.txt
+	@echo "$$FDF_SHORTLOG" >> AUTHORS.txt
+
+
+.PHONY: bump-major
+bump-major: authors ## update AUTHORS and CHANGELOG; bump major version and tag
+	@cp -f CHANGELOG.txt tmp.txt
+	@rm -f CHANGELOG.txt
+	@echo "Release v$(nextmajorversion) -- $(today)\n" > CHANGELOG.txt
+	@git log --oneline `git describe --tags --abbrev=0`..HEAD >> CHANGELOG.txt
+	@echo "\n" >> CHANGELOG.txt
+	@cat tmp.txt >> CHANGELOG.txt
+	@rm -f tmp.txt
+	@git add CHANGELOG.txt AUTHORS.txt
+	@git commit -m "updated CHANGELOG.txt and AUTHORS.txt"
+	@bumpversion major # runs 'git commit' and 'git tag'
+
+
+.PHONY: bump-minor
+bump-minor: authors ## update AUTHORS and CHANGELOG; bump minor version and tag
+	@mv CHANGELOG.txt tmp.txt
+	@echo "Release v$(nextminorversion) -- $(today)\n" > CHANGELOG.txt
+	@git log --oneline `git describe --tags --abbrev=0`..HEAD >> CHANGELOG.txt
+	@echo "\n" >> CHANGELOG.txt
+	@cat tmp.txt >> CHANGELOG.txt
+	@rm -f tmp.txt
+	@git add CHANGELOG.txt AUTHORS.txt
+	@git commit -m "updated CHANGELOG.txt and AUTHORS.txt"
+	@bumpversion minor # runs 'git commit' and 'git tag'
+
+
+.PHONY: bump-patch
+bump-patch: authors ## update AUTHORS and CHANGELOG; bump patch version and tag
+	@cp -f CHANGELOG.txt tmp.txt
+	@rm -f CHANGELOG.txt
+	@echo "Release v$(nextpatchversion) -- $(today)\n" > CHANGELOG.txt
+	@git log --oneline `git describe --tags --abbrev=0`..HEAD >> CHANGELOG.txt
+	@echo "\n" >> CHANGELOG.txt
+	@cat tmp.txt >> CHANGELOG.txt
+	@rm -f tmp.txt
+	@git add CHANGELOG.txt AUTHORS.txt
+	@git commit -m "updated CHANGELOG.txt and AUTHORS.txt"
+	@bumpversion patch # runs 'git commit' and 'git tag'
+
+
+.PHONY: clean
+clean: clean-pyc clean-docs ## remove all build, docs, and Python artifacts
+
+
+.PHONY: clean-docs
+clean-docs: ## remove docs/build
+	rm -rf docs/build
+
+
+.PHONY: clean-pyc
+clean-pyc: ## remove Python file artifacts
+	find . -name '*.pyc' -exec rm -f {} +
+	find . -name '*.pyo' -exec rm -f {} +
+	find . -name '*~' -exec rm -f {} +
+	find . -name '__pycache__' -exec rm -fr {} +