From 95e231004888c358ec5b7ac241fb2bb1eb84fb6e Mon Sep 17 00:00:00 2001 From: Amanda Morin Date: Tue, 19 Jan 2021 10:55:49 -0500 Subject: [PATCH] Added continuous integration --- .flake8 | 12 + .github/workflows/ci-build.yaml | 98 +++++++ .gitignore | 2 + README.md | 2 +- ferminet/__init__.py | 13 + ferminet/configs/__init__.py | 13 + ferminet/hamiltonian.py | 2 +- ferminet/utils/__init__.py | 13 + pylintrc | 448 ++++++++++++++++++++++++++++++++ pytype.cfg | 3 + setup.py | 1 + 11 files changed, 605 insertions(+), 2 deletions(-) create mode 100644 .flake8 create mode 100644 .github/workflows/ci-build.yaml create mode 100644 .gitignore create mode 100644 ferminet/__init__.py create mode 100644 ferminet/configs/__init__.py create mode 100644 ferminet/utils/__init__.py create mode 100644 pylintrc create mode 100644 pytype.cfg diff --git a/.flake8 b/.flake8 new file mode 100644 index 0000000..d257ed8 --- /dev/null +++ b/.flake8 @@ -0,0 +1,12 @@ +[flake8] +max-line-length = 80 +ignore = + C901 # object names too complex + E111, E114 # four-space indents + E121 # line continuations + W503, W504 # line breaks around binary operators +max-complexity = 18 +select = B,C,F,W,T4,B9 +exclude = + .git, + __pycache__ diff --git a/.github/workflows/ci-build.yaml b/.github/workflows/ci-build.yaml new file mode 100644 index 0000000..3160ae6 --- /dev/null +++ b/.github/workflows/ci-build.yaml @@ -0,0 +1,98 @@ +name: CI + +on: + # Trigger the workflow on push or pull request, + # only on the master or jax branches + push: + branches: + - master + - jax + pull_request: + branches: + - master + - jax + workflow_dispatch: + +jobs: + lint_and_typecheck: + runs-on: ubuntu-latest + strategy: + matrix: + python-version: [3.7] + + steps: + - uses: actions/checkout@v2 + - name: Set up Python ${{ matrix.python-version }} + uses: actions/setup-python@v2 + with: + python-version: ${{ matrix.python-version }} + - name: Get pip cache dir + id: pip-cache + run: | + python -m pip install --upgrade pip + echo "::set-output name=dir::$(pip cache dir)" + - name: pip cache + uses: actions/cache@v2 + with: + path: ${{ steps.pip-cache.outputs.dir }} + key: ${{ runner.os }}-pip-${{ hashFiles('**/setup.py') }} + restore-keys: | + ${{ runner.os }}-pip- + - name: Install dependencies + run: | + pip install -e '.[testing]' + - name: Lint with flake8 + run: | + flake8 . + - name: Lint with pylint + run: | + pylint ferminet + - name: Type check with pytype + run: | + pytype ferminet + build: + name: "build ${{ matrix.name-prefix }} (py ${{ matrix.python-version }} on ${{ matrix.os }})" + runs-on: ${{ matrix.os }} + strategy: + matrix: + include: + - name-prefix: "all tests" + python-version: 3.7 + os: ubuntu-latest + package-overrides: "none" + - name-prefix: "all tests" + python-version: 3.8 + os: ubuntu-latest + package-overrides: "none" + - name-prefix: "with internal numpy" + python-version: 3.6 + os: ubuntu-latest + # Test with numpy version that matches Google-internal version + package-overrides: "numpy==1.16.4" + steps: + - uses: actions/checkout@v2 + - name: Set up Python ${{ matrix.python-version }} + uses: actions/setup-python@v2 + with: + python-version: ${{ matrix.python-version }} + - name: Get pip cache dir + id: pip-cache + run: | + python -m pip install --upgrade pip + echo "::set-output name=dir::$(pip cache dir)" + - name: pip cache + uses: actions/cache@v2 + with: + path: ${{ steps.pip-cache.outputs.dir }} + key: ${{ runner.os }}-pip-${{ hashFiles('**/setup.py') }} + restore-keys: | + ${{ runner.os }}-pip- + - name: Install dependencies + run: | + pip install -e '.[testing]' + if [ ${{ matrix.package-overrides }} != none ]; then + pip install ${{ matrix.package-overrides }} + fi + - name: Run tests + run: | + python -m pytest diff --git a/.gitignore b/.gitignore new file mode 100644 index 0000000..7fdea58 --- /dev/null +++ b/.gitignore @@ -0,0 +1,2 @@ +*.pyc +*.egg-info diff --git a/README.md b/README.md index 5c2c7cd..0f5a7cc 100644 --- a/README.md +++ b/README.md @@ -36,7 +36,7 @@ details. The tests are easiest run using pytest: ``` -pip install pytest +pip install -e '.[testing]' python -m pytest ``` diff --git a/ferminet/__init__.py b/ferminet/__init__.py new file mode 100644 index 0000000..f183ac9 --- /dev/null +++ b/ferminet/__init__.py @@ -0,0 +1,13 @@ +# Copyright 2021 DeepMind Technologies Limited. +# +# Licensed under the Apache License, Version 2.0 (the "License"); +# you may not use this file except in compliance with the License. +# You may obtain a copy of the License at +# +# https://www.apache.org/licenses/LICENSE-2.0 +# +# Unless required by applicable law or agreed to in writing, software +# distributed under the License is distributed on an "AS IS" BASIS, +# WITHOUT WARRANTIES OR CONDITIONS OF ANY KIND, either express or implied. +# See the License for the specific language governing permissions and +# limitations under the License. diff --git a/ferminet/configs/__init__.py b/ferminet/configs/__init__.py new file mode 100644 index 0000000..f183ac9 --- /dev/null +++ b/ferminet/configs/__init__.py @@ -0,0 +1,13 @@ +# Copyright 2021 DeepMind Technologies Limited. +# +# Licensed under the Apache License, Version 2.0 (the "License"); +# you may not use this file except in compliance with the License. +# You may obtain a copy of the License at +# +# https://www.apache.org/licenses/LICENSE-2.0 +# +# Unless required by applicable law or agreed to in writing, software +# distributed under the License is distributed on an "AS IS" BASIS, +# WITHOUT WARRANTIES OR CONDITIONS OF ANY KIND, either express or implied. +# See the License for the specific language governing permissions and +# limitations under the License. diff --git a/ferminet/hamiltonian.py b/ferminet/hamiltonian.py index b3e51ff..6d1cbcc 100644 --- a/ferminet/hamiltonian.py +++ b/ferminet/hamiltonian.py @@ -63,7 +63,7 @@ def potential_energy(r_ae, r_ee, atoms, charges): charges: Shape (natoms). Nuclear charges of the atoms. """ v_ee = jnp.sum(jnp.triu(1 / r_ee[..., 0], k=1)) - v_ae = -jnp.sum(charges / r_ae[..., 0]) + v_ae = -jnp.sum(charges / r_ae[..., 0]) # pylint: disable=invalid-unary-operand-type r_aa = jnp.linalg.norm(atoms[None, ...] - atoms[:, None], axis=-1) v_aa = jnp.sum( jnp.triu((charges[None, ...] * charges[..., None]) / r_aa, k=1)) diff --git a/ferminet/utils/__init__.py b/ferminet/utils/__init__.py new file mode 100644 index 0000000..f183ac9 --- /dev/null +++ b/ferminet/utils/__init__.py @@ -0,0 +1,13 @@ +# Copyright 2021 DeepMind Technologies Limited. +# +# Licensed under the Apache License, Version 2.0 (the "License"); +# you may not use this file except in compliance with the License. +# You may obtain a copy of the License at +# +# https://www.apache.org/licenses/LICENSE-2.0 +# +# Unless required by applicable law or agreed to in writing, software +# distributed under the License is distributed on an "AS IS" BASIS, +# WITHOUT WARRANTIES OR CONDITIONS OF ANY KIND, either express or implied. +# See the License for the specific language governing permissions and +# limitations under the License. diff --git a/pylintrc b/pylintrc new file mode 100644 index 0000000..c19721a --- /dev/null +++ b/pylintrc @@ -0,0 +1,448 @@ +# This Pylint rcfile contains a best-effort configuration to uphold the +# best-practices and style described in the Google Python style guide: +# https://google.github.io/styleguide/pyguide.html +# +# Its canonical open-source location is: +# https://google.github.io/styleguide/pylintrc + +[MASTER] + +# Add files or directories to the blacklist. They should be base names, not +# paths. +ignore=third_party + +# Add files or directories matching the regex patterns to the blacklist. The +# regex matches against base names, not paths. +ignore-patterns= + +# Pickle collected data for later comparisons. +persistent=no + +# List of plugins (as comma separated values of python modules names) to load, +# usually to register additional checkers. +load-plugins= + +# Use multiple processes to speed up Pylint. +jobs=4 + +# Allow loading of arbitrary C extensions. Extensions are imported into the +# active Python interpreter and may run arbitrary code. +unsafe-load-any-extension=no + +# A comma-separated list of package or module names from where C extensions may +# be loaded. Extensions are loading into the active Python interpreter and may +# run arbitrary code +extension-pkg-whitelist= + + +[MESSAGES CONTROL] + +# Only show warnings with the listed confidence levels. Leave empty to show +# all. Valid levels: HIGH, INFERENCE, INFERENCE_FAILURE, UNDEFINED +confidence= + +# Enable the message, report, category or checker with the given id(s). You can +# either give multiple identifier separated by comma (,) or put this option +# multiple time (only on the command line, not in the configuration file where +# it should appear only once). See also the "--disable" option for examples. +#enable= + +# Disable the message, report, category or checker with the given id(s). You +# can either give multiple identifiers separated by comma (,) or put this +# option multiple times (only on the command line, not in the configuration +# file where it should appear only once).You can also use "--disable=all" to +# disable everything first and then reenable specific checks. For example, if +# you want to run only the similarities checker, you can use "--disable=all +# --enable=similarities". If you want to run only the classes checker, but have +# no Warning level messages displayed, use"--disable=all --enable=classes +# --disable=W" +disable=abstract-method, + apply-builtin, + arguments-differ, + attribute-defined-outside-init, + backtick, + bad-option-value, + basestring-builtin, + buffer-builtin, + c-extension-no-member, + consider-using-enumerate, + cmp-builtin, + cmp-method, + coerce-builtin, + coerce-method, + delslice-method, + div-method, + duplicate-code, + eq-without-hash, + execfile-builtin, + file-builtin, + filter-builtin-not-iterating, + fixme, + getslice-method, + global-statement, + hex-method, + idiv-method, + implicit-str-concat-in-sequence, + import-error, + import-self, + import-star-module-level, + inconsistent-return-statements, + input-builtin, + intern-builtin, + invalid-str-codec, + locally-disabled, + long-builtin, + long-suffix, + map-builtin-not-iterating, + misplaced-comparison-constant, + missing-function-docstring, + metaclass-assignment, + next-method-called, + next-method-defined, + no-absolute-import, + no-else-break, + no-else-continue, + no-else-raise, + no-else-return, + no-init, # added + no-member, + no-name-in-module, + no-self-use, + nonzero-method, + oct-method, + old-division, + old-ne-operator, + old-octal-literal, + old-raise-syntax, + parameter-unpacking, + print-statement, + raising-string, + range-builtin-not-iterating, + raw_input-builtin, + rdiv-method, + reduce-builtin, + relative-import, + reload-builtin, + round-builtin, + setslice-method, + signature-differs, + standarderror-builtin, + suppressed-message, + sys-max-int, + too-few-public-methods, + too-many-ancestors, + too-many-arguments, + too-many-boolean-expressions, + too-many-branches, + too-many-instance-attributes, + too-many-locals, + too-many-nested-blocks, + too-many-public-methods, + too-many-return-statements, + too-many-statements, + trailing-newlines, + unichr-builtin, + unicode-builtin, + unnecessary-pass, + unpacking-in-except, + useless-else-on-loop, + useless-object-inheritance, + useless-suppression, + using-cmp-argument, + wrong-import-order, + xrange-builtin, + zip-builtin-not-iterating, + line-too-long, # line too long error, caught with flake8 + + +[REPORTS] + +# Set the output format. Available formats are text, parseable, colorized, msvs +# (visual studio) and html. You can also give a reporter class, eg +# mypackage.mymodule.MyReporterClass. +output-format=text + +# Put messages in a separate file for each module / package specified on the +# command line instead of printing them on stdout. Reports (if any) will be +# written in a file name "pylint_global.[txt|html]". This option is deprecated +# and it will be removed in Pylint 2.0. +files-output=no + +# Tells whether to display a full report or only the messages +reports=no + +# Python expression which should return a note less than 10 (10 is the highest +# note). You have access to the variables errors warning, statement which +# respectively contain the number of errors / warnings messages and the total +# number of statements analyzed. This is used by the global evaluation report +# (RP0004). +evaluation=10.0 - ((float(5 * error + warning + refactor + convention) / statement) * 10) + +# Template used to display messages. This is a python new-style format string +# used to format the message information. See doc for all details +#msg-template= + + +[BASIC] + +# Good variable names which should always be accepted, separated by a comma +good-names=main,_ + +# Bad variable names which should always be refused, separated by a comma +bad-names= + +# Colon-delimited sets of names that determine each other's naming style when +# the name regexes allow several styles. +name-group= + +# Include a hint for the correct naming format with invalid-name +include-naming-hint=no + +# List of decorators that produce properties, such as abc.abstractproperty. Add +# to this list to register other decorators that produce valid properties. +property-classes=abc.abstractproperty,cached_property.cached_property,cached_property.threaded_cached_property,cached_property.cached_property_with_ttl,cached_property.threaded_cached_property_with_ttl + +# Regular expression matching correct function names +function-rgx=^(?:(?PsetUp|tearDown|setUpModule|tearDownModule)|(?P_?[A-Z][a-zA-Z0-9]*)|(?P_?[a-z][a-z0-9_]*))$ + +# Regular expression matching correct variable names +variable-rgx=^[a-z][a-z0-9_]*$ + +# Regular expression matching correct constant names +const-rgx=^(_?[A-Z][A-Z0-9_]*|__[a-z0-9_]+__|_?[a-z][a-z0-9_]*)$ + +# Regular expression matching correct attribute names +attr-rgx=^_{0,2}[a-z][a-z0-9_]*$ + +# Regular expression matching correct argument names +argument-rgx=^[a-z][a-z0-9_]*$ + +# Regular expression matching correct class attribute names +class-attribute-rgx=^(_?[A-Z][A-Z0-9_]*|__[a-z0-9_]+__|_?[a-z][a-z0-9_]*)$ + +# Regular expression matching correct inline iteration names +inlinevar-rgx=^[a-z][a-z0-9_]*$ + +# Regular expression matching correct class names +class-rgx=^_?[A-Z][a-zA-Z0-9]*$ + +# Regular expression matching correct module names +module-rgx=^(_?[a-z][a-z0-9_]*|__init__)$ + +# Regular expression matching correct method names +method-rgx=(?x)^(?:(?P_[a-z0-9_]+__|runTest|setUp|tearDown|setUpTestCase|tearDownTestCase|setupSelf|tearDownClass|setUpClass|(test|assert)_*[A-Z0-9][a-zA-Z0-9_]*|next)|(?P_{0,2}[A-Z][a-zA-Z0-9_]*)|(?P_{0,2}[a-z][a-z0-9_]*))$ + +# Regular expression which should only match function or class names that do +# not require a docstring. +no-docstring-rgx=(__.*__|main|test.*|.*test|.*Test)$ + +# Minimum line length for functions/classes that require docstrings, shorter +# ones are exempt. +docstring-min-length=10 + + +[TYPECHECK] + +# List of decorators that produce context managers, such as +# contextlib.contextmanager. Add to this list to register other decorators that +# produce valid context managers. +contextmanager-decorators=contextlib.contextmanager,contextlib2.contextmanager + +# Tells whether missing members accessed in mixin class should be ignored. A +# mixin class is detected if its name ends with "mixin" (case insensitive). +ignore-mixin-members=yes + +# List of module names for which member attributes should not be checked +# (useful for modules/projects where namespaces are manipulated during runtime +# and thus existing member attributes cannot be deduced by static analysis. It +# supports qualified module names, as well as Unix pattern matching. +ignored-modules= + +# List of class names for which member attributes should not be checked (useful +# for classes with dynamically set attributes). This supports the use of +# qualified names. +ignored-classes=optparse.Values,thread._local,_thread._local + +# List of members which are set dynamically and missed by pylint inference +# system, and so shouldn't trigger E1101 when accessed. Python regular +# expressions are accepted. +generated-members= + + +[FORMAT] + +# Maximum number of characters on a single line. +max-line-length=80 + +# TODO(https://github.com/PyCQA/pylint/issues/3352): Direct pylint to exempt +# lines made too long by directives to pytype. + +# Regexp for a line that is allowed to be longer than the limit. +ignore-long-lines=(?x)( + ^\s*(\#\ )??$| + ^\s*(from\s+\S+\s+)?import\s+.+$) + +# Allow the body of an if to be on the same line as the test if there is no +# else. +single-line-if-stmt=yes + +# List of optional constructs for which whitespace checking is disabled. `dict- +# separator` is used to allow tabulation in dicts, etc.: {1 : 1,\n222: 2}. +# `trailing-comma` allows a space between comma and closing bracket: (a, ). +# `empty-line` allows space-only lines. +no-space-check= + +# Maximum number of lines in a module +max-module-lines=99999 + +# String used as indentation unit. The internal Google style guide mandates 2 +# spaces. Google's externaly-published style guide says 4, consistent with +# PEP 8. Here, we use 2 spaces, for conformity with many open-sourced Google +# projects (like TensorFlow). +indent-string=' ' + +# Number of spaces of indent required inside a hanging or continued line. +indent-after-paren=4 + +# Expected format of line ending, e.g. empty (any line ending), LF or CRLF. +expected-line-ending-format= + + +[MISCELLANEOUS] + +# List of note tags to take in consideration, separated by a comma. +notes=TODO + + +[STRING] + +# This flag controls whether inconsistent-quotes generates a warning when the +# character used as a quote delimiter is used inconsistently within a module. +check-quote-consistency=yes + + +[VARIABLES] + +# Tells whether we should check for unused import in __init__ files. +init-import=no + +# A regular expression matching the name of dummy variables (i.e. expectedly +# not used). +dummy-variables-rgx=^\*{0,2}(_$|unused_|dummy_) + +# List of additional names supposed to be defined in builtins. Remember that +# you should avoid to define new builtins when possible. +additional-builtins= + +# List of strings which can identify a callback function by name. A callback +# name must start or end with one of those strings. +callbacks=cb_,_cb + +# List of qualified module names which can have objects that can redefine +# builtins. +redefining-builtins-modules=six,six.moves,past.builtins,future.builtins,functools + + +[LOGGING] + +# Logging modules to check that the string format arguments are in logging +# function parameter format +logging-modules=logging,absl.logging,tensorflow.io.logging + + +[SIMILARITIES] + +# Minimum lines number of a similarity. +min-similarity-lines=4 + +# Ignore comments when computing similarities. +ignore-comments=yes + +# Ignore docstrings when computing similarities. +ignore-docstrings=yes + +# Ignore imports when computing similarities. +ignore-imports=no + + +[SPELLING] + +# Spelling dictionary name. Available dictionaries: none. To make it working +# install python-enchant package. +spelling-dict= + +# List of comma separated words that should not be checked. +spelling-ignore-words= + +# A path to a file that contains private dictionary; one word per line. +spelling-private-dict-file= + +# Tells whether to store unknown words to indicated private dictionary in +# --spelling-private-dict-file option instead of raising a message. +spelling-store-unknown-words=no + + +[IMPORTS] + +# Deprecated modules which should not be used, separated by a comma +deprecated-modules=regsub, + TERMIOS, + Bastion, + rexec, + sets + +# Create a graph of every (i.e. internal and external) dependencies in the +# given file (report RP0402 must not be disabled) +import-graph= + +# Create a graph of external dependencies in the given file (report RP0402 must +# not be disabled) +ext-import-graph= + +# Create a graph of internal dependencies in the given file (report RP0402 must +# not be disabled) +int-import-graph= + +# Force import order to recognize a module as part of the standard +# compatibility libraries. +known-standard-library= + +# Force import order to recognize a module as part of a third party library. +known-third-party=enchant, absl + +# Analyse import fallback blocks. This can be used to support both Python 2 and +# 3 compatible code, which means that the block might have code that exists +# only in one or another interpreter, leading to false positives when analysed. +analyse-fallback-blocks=no + + +[CLASSES] + +# List of method names used to declare (i.e. assign) instance attributes. +defining-attr-methods=__init__, + __new__, + setUp + +# List of member names, which should be excluded from the protected access +# warning. +exclude-protected=_asdict, + _fields, + _replace, + _source, + _make + +# List of valid names for the first argument in a class method. +valid-classmethod-first-arg=cls, + class_ + +# List of valid names for the first argument in a metaclass class method. +valid-metaclass-classmethod-first-arg=mcs + + +[EXCEPTIONS] + +# Exceptions that will emit a warning when being caught. Defaults to +# "Exception" +overgeneral-exceptions=StandardError, + Exception, + BaseException \ No newline at end of file diff --git a/pytype.cfg b/pytype.cfg new file mode 100644 index 0000000..01c32cd --- /dev/null +++ b/pytype.cfg @@ -0,0 +1,3 @@ +[pytype] +inputs = ferminet +disable = wrong-arg-types \ No newline at end of file diff --git a/setup.py b/setup.py index 708f83e..37f0c36 100644 --- a/setup.py +++ b/setup.py @@ -53,6 +53,7 @@ def ferminet_test_suite(): scripts=['bin/ferminet'], packages=find_packages(), install_requires=REQUIRED_PACKAGES, + extras_require={'testing': ['flake8', 'pylint', 'pytest', 'pytype']}, platforms=['any'], license='Apache 2.0', test_suite='setup.ferminet_test_suite',