diff --git a/.travis.yml b/.travis.yml deleted file mode 100644 index 7788579d62d12f1c0af5098f1d93e5b8cb26be21..0000000000000000000000000000000000000000 --- a/.travis.yml +++ /dev/null @@ -1,29 +0,0 @@ -# Config file for automatic testing at travis-ci.org - -language: python -python: - - 3.6 - - 3.5 - - 3.4 - - 2.7 - -# Command to install dependencies, e.g. pip install -r requirements.txt --use-mirrors -install: pip install -U tox-travis - -# Command to run tests, e.g. python setup.py test -script: tox - -# Assuming you have installed the travis-ci CLI tool, after you -# create the Github repo and add it to Travis, run the -# following command to finish PyPI deployment setup: -# $ travis encrypt --add deploy.password -deploy: - provider: pypi - distributions: sdist bdist_wheel - user: robet.rosca - password: - secure: PLEASE_REPLACE_ME - on: - tags: true - repo: robet.rosca/karabo_data_interactive - python: 3.6 diff --git a/AUTHORS.rst b/AUTHORS.rst deleted file mode 100644 index 9302fb0dbc915e01519fdcca593e79124629de89..0000000000000000000000000000000000000000 --- a/AUTHORS.rst +++ /dev/null @@ -1,13 +0,0 @@ -======= -Credits -======= - -Development Lead ----------------- - -* Robert Rosca <robert.rosca@xfel.eu> - -Contributors ------------- - -None yet. Why not be the first? diff --git a/CONTRIBUTING.rst b/CONTRIBUTING.rst deleted file mode 100644 index f5de07bfa5eeea3bdfd5c172aa16141f5b9d214d..0000000000000000000000000000000000000000 --- a/CONTRIBUTING.rst +++ /dev/null @@ -1,128 +0,0 @@ -.. highlight:: shell - -============ -Contributing -============ - -Contributions are welcome, and they are greatly appreciated! Every little bit -helps, and credit will always be given. - -You can contribute in many ways: - -Types of Contributions ----------------------- - -Report Bugs -~~~~~~~~~~~ - -Report bugs at https://github.com/robet.rosca/karabo_data_interactive/issues. - -If you are reporting a bug, please include: - -* Your operating system name and version. -* Any details about your local setup that might be helpful in troubleshooting. -* Detailed steps to reproduce the bug. - -Fix Bugs -~~~~~~~~ - -Look through the GitHub issues for bugs. Anything tagged with "bug" and "help -wanted" is open to whoever wants to implement it. - -Implement Features -~~~~~~~~~~~~~~~~~~ - -Look through the GitHub issues for features. Anything tagged with "enhancement" -and "help wanted" is open to whoever wants to implement it. - -Write Documentation -~~~~~~~~~~~~~~~~~~~ - -Karabo Data Interactive could always use more documentation, whether as part of the -official Karabo Data Interactive docs, in docstrings, or even on the web in blog posts, -articles, and such. - -Submit Feedback -~~~~~~~~~~~~~~~ - -The best way to send feedback is to file an issue at https://github.com/robet.rosca/karabo_data_interactive/issues. - -If you are proposing a feature: - -* Explain in detail how it would work. -* Keep the scope as narrow as possible, to make it easier to implement. -* Remember that this is a volunteer-driven project, and that contributions - are welcome :) - -Get Started! ------------- - -Ready to contribute? Here's how to set up `karabo_data_interactive` for local development. - -1. Fork the `karabo_data_interactive` repo on GitHub. -2. Clone your fork locally:: - - $ git clone git@github.com:your_name_here/karabo_data_interactive.git - -3. Install your local copy into a virtualenv. Assuming you have virtualenvwrapper installed, this is how you set up your fork for local development:: - - $ mkvirtualenv karabo_data_interactive - $ cd karabo_data_interactive/ - $ python setup.py develop - -4. Create a branch for local development:: - - $ git checkout -b name-of-your-bugfix-or-feature - - Now you can make your changes locally. - -5. When you're done making changes, check that your changes pass flake8 and the - tests, including testing other Python versions with tox:: - - $ flake8 karabo_data_interactive tests - $ python setup.py test or py.test - $ tox - - To get flake8 and tox, just pip install them into your virtualenv. - -6. Commit your changes and push your branch to GitHub:: - - $ git add . - $ git commit -m "Your detailed description of your changes." - $ git push origin name-of-your-bugfix-or-feature - -7. Submit a pull request through the GitHub website. - -Pull Request Guidelines ------------------------ - -Before you submit a pull request, check that it meets these guidelines: - -1. The pull request should include tests. -2. If the pull request adds functionality, the docs should be updated. Put - your new functionality into a function with a docstring, and add the - feature to the list in README.rst. -3. The pull request should work for Python 2.7, 3.4, 3.5 and 3.6, and for PyPy. Check - https://travis-ci.org/robet.rosca/karabo_data_interactive/pull_requests - and make sure that the tests pass for all supported Python versions. - -Tips ----- - -To run a subset of tests:: - - - $ python -m unittest tests.test_karabo_data_interactive - -Deploying ---------- - -A reminder for the maintainers on how to deploy. -Make sure all your changes are committed (including an entry in HISTORY.rst). -Then run:: - -$ bumpversion patch # possible: major / minor / patch -$ git push -$ git push --tags - -Travis will then deploy to PyPI if tests pass. diff --git a/HISTORY.rst b/HISTORY.rst index b1d9b8639820f54aacbb36a117d4cffcad1fce83..efff4978b9b4307d9902018b7e592e2a6a8fcaab 100644 --- a/HISTORY.rst +++ b/HISTORY.rst @@ -5,7 +5,7 @@ History 0.1.0 (2019-01-30) ------------------ -* First release on PyPI +* First release 0.1.1 (2019-02-14) ------------------ @@ -14,11 +14,18 @@ Major changes: * Error handling for missing image information in a train * Supportive functions for the error handling: - * `nanfull_stack`, `_status_image_*` + * `nanfull_stack`, `_find_good_trains` * Widgets for skipping to next train with image information - * `widget_status_type`, `widget_status_info`, `widget_next_good_id` + * `widget_prev_good`, `widget_next_good`, `widget_status` Minor: * Improved quickstart guide * Update setup script and guide with new module paths + +0.1.2 (2019-03-06) +------------------ + +Minor: + +* Fix bug where non-detector devices were being searched by the '_find_good_trains` function \ No newline at end of file diff --git a/MANIFEST.in b/MANIFEST.in deleted file mode 100644 index 965b2dda7db7c49f68857dc3aea9af37e30a745e..0000000000000000000000000000000000000000 --- a/MANIFEST.in +++ /dev/null @@ -1,11 +0,0 @@ -include AUTHORS.rst -include CONTRIBUTING.rst -include HISTORY.rst -include LICENSE -include README.rst - -recursive-include tests * -recursive-exclude * __pycache__ -recursive-exclude * *.py[co] - -recursive-include docs *.rst conf.py Makefile make.bat *.jpg *.png *.gif diff --git a/Makefile b/Makefile deleted file mode 100644 index 031458767fac6a88fafecbed46de559201a168d0..0000000000000000000000000000000000000000 --- a/Makefile +++ /dev/null @@ -1,88 +0,0 @@ -.PHONY: clean clean-test clean-pyc clean-build docs help -.DEFAULT_GOAL := help - -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 - -define PRINT_HELP_PYSCRIPT -import re, sys - -for line in sys.stdin: - match = re.match(r'^([a-zA-Z_-]+):.*?## (.*)$$', line) - if match: - target, help = match.groups() - print("%-20s %s" % (target, help)) -endef -export PRINT_HELP_PYSCRIPT - -BROWSER := python -c "$$BROWSER_PYSCRIPT" - -help: - @python -c "$$PRINT_HELP_PYSCRIPT" < $(MAKEFILE_LIST) - -clean: clean-build clean-pyc clean-test ## remove all build, test, coverage and Python artifacts - -clean-build: ## remove build artifacts - rm -fr build/ - rm -fr dist/ - rm -fr .eggs/ - find . \( -path ./env -o -path ./venv -o -path ./.env -o -path ./.venv \) -prune -o -name '*.egg-info' -exec rm -fr {} + - find . \( -path ./env -o -path ./venv -o -path ./.env -o -path ./.venv \) -prune -o -name '*.egg' -exec rm -f {} + - -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 {} + - -clean-test: ## remove test and coverage artifacts - rm -fr .tox/ - rm -f .coverage - rm -fr htmlcov/ - rm -fr .pytest_cache - -lint: ## check style with flake8 - flake8 karabo_data_interactive tests - -test: ## run tests quickly with the default Python - python setup.py test - -test-all: ## run tests on every Python version with tox - tox - -coverage: ## check code coverage quickly with the default Python - coverage run --source karabo_data_interactive setup.py test - coverage report -m - coverage html - $(BROWSER) htmlcov/index.html - -docs: ## generate Sphinx HTML documentation, including API docs - rm -f docs/karabo_data_interactive.rst - rm -f docs/modules.rst - sphinx-apidoc -o docs/ karabo_data_interactive - $(MAKE) -C docs clean - $(MAKE) -C docs html - $(BROWSER) docs/_build/html/index.html - -servedocs: docs ## compile the docs watching for changes - watchmedo shell-command -p '*.rst' -c '$(MAKE) -C docs html' -R -D . - -release: dist ## package and upload a release - twine upload dist/* - -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 diff --git a/Pipfile b/Pipfile deleted file mode 100644 index 316f86467f3a0bba685529e361a6bc148d88536f..0000000000000000000000000000000000000000 --- a/Pipfile +++ /dev/null @@ -1,18 +0,0 @@ -[[source]] -url = "https://pypi.python.org/simple" -verify_ssl = true - -[dev-packages] -pipenv = "*" -setuptools = "*" -wheel = "*" -pip2pi = "*" -nbval = "*" - -[packages] -karabo-data = {git = "https://github.com/European-XFEL/karabo_data",editable = true} -ipywidgets = "*" -karabo-data-interactive = {path = ".",editable = true} -watermark = "*" -cookiecutter = "*" -ipykernel = "*" diff --git a/Pipfile.lock b/Pipfile.lock deleted file mode 100644 index 9310163e6dbde497db00e52821d224c9cac3b9a8..0000000000000000000000000000000000000000 --- a/Pipfile.lock +++ /dev/null @@ -1,1021 +0,0 @@ -{ - 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for source_name, source_files in self.run._source_index.items(): - good_trains_source = [] - for file in source_files: - good_trains_source += \ - set(file.train_ids[file.get_index(source_name, 'image')[1].nonzero()]) + for source_name in self.run_image_selection.all_sources: + good_trains_source = set() + for source_file in self.run_image_selection._source_index[source_name]: + good_trains_source.update( + set(source_file.train_ids[source_file.get_index(source_name, 'image')[1].nonzero()]) + ) trains_with_images[source_name] = good_trains_source self.good_trains_per_source = trains_with_images - self.good_trains = reduce(np.intersect1d, list(trains_with_images.values())) + self.good_trains = reduce(set.intersection, list(trains_with_images.values())) def init_plot(self, train_index=None, pulse_index=None, clip_range=None, cmap='viridis', image_type=None): diff --git a/setup.cfg b/setup.cfg index 6188cb17d98640a5afa88decd9663837e92a489b..3ee8ddf09e05543db89c6786dcd07e59ead8f9aa 100644 --- a/setup.cfg +++ b/setup.cfg @@ -1,5 +1,5 @@ [bumpversion] -current_version = 0.1.1 +current_version = 0.1.2 commit = True tag = True @@ -19,15 +19,13 @@ exclude = docs max-line-length = 100 [coverage:run] -source = - karabo_data_interactive - -omit = - env/* - venv/* - .env/* - .venv/* +source = + karabo_data_interactive +omit = + env/* + venv/* + .env/* + .venv/* [aliases] -# Define setup.py command aliases here diff --git a/setup.py b/setup.py index 029a3e832bfa0b0aeb3a2ba427a5813742de5518..7b18965bd1f3aa0dd41b00343989bb5df85f7729 100644 --- a/setup.py +++ b/setup.py @@ -49,6 +49,6 @@ setup( test_suite='tests', tests_require=test_requirements, url='https://github.com/robet.rosca/karabo_data_interactive', - version='0.1.1', + version='0.1.2', zip_safe=False, ) diff --git a/tests/__init__.py b/tests/__init__.py deleted file mode 100644 index 36e29886077f3341dfcf77397b12a6690c72e67c..0000000000000000000000000000000000000000 --- a/tests/__init__.py +++ /dev/null @@ -1,3 +0,0 @@ -# -*- coding: utf-8 -*- - -"""Unit test package for karabo_data_interactive.""" diff --git a/tests/test_karabo_data_interactive.py b/tests/test_karabo_data_interactive.py deleted file mode 100644 index 56bfa6e18ea4db24ae45f2662aac45bd507f95cc..0000000000000000000000000000000000000000 --- a/tests/test_karabo_data_interactive.py +++ /dev/null @@ -1,22 +0,0 @@ -#!/usr/bin/env python -# -*- coding: utf-8 -*- - -"""Tests for `karabo_data_interactive` package.""" - - -import unittest - -from karabo_data_interactive import karabo_data_interactive - - -class TestKarabo_data_interactive(unittest.TestCase): - """Tests for `karabo_data_interactive` package.""" - - def setUp(self): - """Set up test fixtures, if any.""" - - def tearDown(self): - """Tear down test fixtures, if any.""" - - def test_000_something(self): - """Test something.""" diff --git a/tox.ini b/tox.ini deleted file mode 100644 index d10beeed22320e4ff6f81a80cf7d3aba44b8d5fe..0000000000000000000000000000000000000000 --- a/tox.ini +++ /dev/null @@ -1,19 +0,0 @@ -[tox] -envlist = py27, py34, py35, py36, flake8 - -[travis] -python = - 3.6: py36 - 3.5: py35 - 3.4: py34 - 2.7: py27 - -[testenv:flake8] -basepython = python -deps = flake8 -commands = flake8 karabo_data_interactive - -[testenv] - -commands = python setup.py test - diff --git a/travis_pypi_setup.py b/travis_pypi_setup.py deleted file mode 100644 index a1fe4148b08a7add7debec6295d8b0ffa201e7cd..0000000000000000000000000000000000000000 --- a/travis_pypi_setup.py +++ /dev/null @@ -1,122 +0,0 @@ -#!/usr/bin/env python -# -*- coding: utf-8 -*- -"""Update encrypted deploy password in Travis config file -""" - - -from __future__ import print_function -import base64 -import json -import os -from getpass import getpass -import yaml -from cryptography.hazmat.primitives.serialization import load_pem_public_key -from cryptography.hazmat.backends import default_backend -from cryptography.hazmat.primitives.asymmetric.padding import PKCS1v15 - - -try: - from urllib import urlopen -except: - from urllib.request import urlopen - - -GITHUB_REPO = 'robet.rosca/karabo_data_interactive' -TRAVIS_CONFIG_FILE = os.path.join( - os.path.dirname(os.path.abspath(__file__)), '.travis.yml') - - -def load_key(pubkey): - """Load public RSA key, with work-around for keys using - incorrect header/footer format. - - Read more about RSA encryption with cryptography: - https://cryptography.io/latest/hazmat/primitives/asymmetric/rsa/ - """ - try: - return load_pem_public_key(pubkey.encode(), default_backend()) - except ValueError: - # workaround for https://github.com/travis-ci/travis-api/issues/196 - pubkey = pubkey.replace('BEGIN RSA', 'BEGIN').replace('END RSA', 'END') - return load_pem_public_key(pubkey.encode(), default_backend()) - - -def encrypt(pubkey, password): - """Encrypt password using given RSA public key and encode it with base64. - - The encrypted password can only be decrypted by someone with the - private key (in this case, only Travis). - """ - key = load_key(pubkey) - encrypted_password = key.encrypt(password, PKCS1v15()) - return base64.b64encode(encrypted_password) - - -def fetch_public_key(repo): - """Download RSA public key Travis will use for this repo. - - Travis API docs: http://docs.travis-ci.com/api/#repository-keys - """ - keyurl = 'https://api.travis-ci.org/repos/{0}/key'.format(repo) - data = json.loads(urlopen(keyurl).read().decode()) - if 'key' not in data: - errmsg = "Could not find public key for repo: {}.\n".format(repo) - errmsg += "Have you already added your GitHub repo to Travis?" - raise ValueError(errmsg) - return data['key'] - - -def prepend_line(filepath, line): - """Rewrite a file adding a line to its beginning. - """ - with open(filepath) as f: - lines = f.readlines() - - lines.insert(0, line) - - with open(filepath, 'w') as f: - f.writelines(lines) - - -def load_yaml_config(filepath): - with open(filepath) as f: - return yaml.load(f) - - -def save_yaml_config(filepath, config): - with open(filepath, 'w') as f: - yaml.dump(config, f, default_flow_style=False) - - -def update_travis_deploy_password(encrypted_password): - """Update the deploy section of the .travis.yml file - to use the given encrypted password. - """ - config = load_yaml_config(TRAVIS_CONFIG_FILE) - - config['deploy']['password'] = dict(secure=encrypted_password) - - save_yaml_config(TRAVIS_CONFIG_FILE, config) - - line = ('# This file was autogenerated and will overwrite' - ' each time you run travis_pypi_setup.py\n') - prepend_line(TRAVIS_CONFIG_FILE, line) - - -def main(args): - public_key = fetch_public_key(args.repo) - password = args.password or getpass('PyPI password: ') - update_travis_deploy_password(encrypt(public_key, password.encode())) - print("Wrote encrypted password to .travis.yml -- you're ready to deploy") - - -if '__main__' == __name__: - import argparse - parser = argparse.ArgumentParser(description=__doc__) - parser.add_argument('--repo', default=GITHUB_REPO, - help='GitHub repo (default: %s)' % GITHUB_REPO) - parser.add_argument('--password', - help='PyPI password (will prompt if not provided)') - - args = parser.parse_args() - main(args)