diff --git a/.github/workflows/ci.yml b/.github/workflows/ci.yml new file mode 100644 index 0000000..38460c5 --- /dev/null +++ b/.github/workflows/ci.yml @@ -0,0 +1,106 @@ +name: CI + +on: + push: + branches: [ master ] + pull_request: + branches: [ master ] + + +jobs: + Quality: + runs-on: ubuntu-latest + strategy: + fail-fast: true + matrix: + python-version: ["3.8", "3.9", "3.10"] + + steps: + - uses: actions/checkout@v3 + + - uses: actions/setup-python@v3 + with: + python-version: ${{matrix.python-version}} + + - name: Install Python Poetry + uses: abatilo/actions-poetry@v2.3.0 + + - name: Configure poetry + shell: bash + run: python -m poetry config virtualenvs.in-project true + + - name: View poetry version + run: poetry --version + + - name: Install dependencies + run: | + python -m poetry install + + - name: Test + run: poetry run python3 -m unittest discover + + Release: + needs: Quality + if: | + github.event_name == 'push' && + github.ref == 'refs/heads/master' && + !contains ( github.event.head_commit.message, 'chore(release)' ) + + runs-on: ubuntu-latest + concurrency: release + permissions: + id-token: write + contents: write + + steps: + - uses: actions/setup-python@v3 + with: + python-version: 3.8 + + - uses: actions/checkout@v3 + with: + fetch-depth: 0 + + - name: Check release status + id: release-status + env: + GH_TOKEN: ${{ secrets.GITHUB_TOKEN }} + run: | + pip install python-semantic-release + if semantic-release --noop --strict version + then + echo "Releasing new version." + else + echo "Skipping release steps." + fi + + - if: steps.release-status.outputs.released == 'true' + name: Release to GitHub + id: github-release + env: + GH_TOKEN: ${{ secrets.GITHUB_TOKEN }} + run: | + semantic-release version + git fetch --tags + for file in ./dist/** + do gh release upload "${{steps.release-status.outputs.tag}}" $file + done + + - if: steps.release-status.outputs.released == 'true' + name: Release to Test PyPI + id: test-pypi-release + env: + TEST_PYPI_TOKEN: ${{ secrets.TEST_PYPI_TOKEN }} + run: | + poetry config repositories.test-pypi https://test.pypi.org/legacy/ + poetry config pypi-token.test-pypi $TEST_PYPI_TOKEN + poetry publish -r test-pypi -u __token__ + + - if: false && steps.release-status.outputs.released == 'true' + name: Release to PyPI + id: pypi-release + env: + PYPI_TOKEN: ${{ secrets.PYPI_TOKEN }} + run: | + poetry config pypi-token.pypi $PYPI_TOKEN + poetry publish diff --git a/.pylintrc b/.pylintrc deleted file mode 100644 index 18f6478..0000000 --- a/.pylintrc +++ /dev/null @@ -1,448 +0,0 @@ -# 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=16 - -# 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, - - -[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 - diff --git a/.travis.yml b/.travis.yml deleted file mode 100644 index 341af6b..0000000 --- a/.travis.yml +++ /dev/null @@ -1,22 +0,0 @@ -language: python -python: - - "3.6" # current default Python on Travis CI - - "3.7" - - "3.8" -os: - - linux -# command to install dependencies -install: - - pip install -r requirements.txt - - pip install --upgrade pytest - - pip install pylint==2.5.3 - - pip install pytest-cov - -# command to run tests -script: - - python -m pytest tests/ --cov - - pylint --fail-under=8 dsm/ - -#command to track code coverage -after_success: - - bash <(curl -s https://codecov.io/bash) diff --git a/README.md b/README.md index 966e237..583e7e6 100644 --- a/README.md +++ b/README.md @@ -1,10 +1,12 @@ -visitor badge     [![codecov](https://codecov.io/gh/autonlab/DeepSurvivalMachines/branch/master/graph/badge.svg?token=FU1HB5O92D)](https://codecov.io/gh/autonlab/DeepSurvivalMachines)     [![License: MIT](https://img.shields.io/badge/License-MIT-yellow.svg)](https://opensource.org/licenses/MIT)     [![GitHub Repo stars](https://img.shields.io/github/stars/autonlab/auton-survival?style=social)](https://github.com/autonlab/auton-survival) +    +![CI](https://github.com/autonlab/auton-survival/actions/workflows/ci.yml/badge.svg) + diff --git a/auton_survival/__init__.py b/auton_survival/__init__.py index 56bfe9b..6a021d6 100644 --- a/auton_survival/__init__.py +++ b/auton_survival/__init__.py @@ -468,9 +468,6 @@ class is a composite transform that does both Imputing ***and*** Scaling with ''' -__version__ = "0.1.0" - - from .models.dsm import DeepSurvivalMachines from .models.dcm import DeepCoxMixtures from .models.cph import DeepCoxPH, DeepRecurrentCoxPH diff --git a/pyproject.toml b/pyproject.toml new file mode 100644 index 0000000..7e22fcf --- /dev/null +++ b/pyproject.toml @@ -0,0 +1,50 @@ +[tool.poetry] +name = "auton-survival" +version = "0.1.0" +description = "" +authors = ["Chirag Nagpal "] +readme = "README.md" +packages = [{include = "auton_survival"}] + +[tool.poetry.dependencies] +python = "^3.8" +torch = "^1.13" +numpy = "^1.24" +pandas = "^1.5" +tqdm = "^4.66" +scikit-learn = "^1.2" +torchvision = "^0.14" +scikit-survival = "^0.21" +lifelines = "^0.26" + +[tool.semantic_release] +version_toml = [ + "pyproject.toml:tool.poetry.version" +] +branch = "master" +commit_author = "github-actions[bot] <41898282+github-actions[bot]@users.noreply.github.com>" +upload_to_PyPI = false +upload_to_release = true +build_command = "pip install poetry && poetry build" + +[tool.semantic_release.commit_parser_options] +allowed_tags = [ + "build", + "chore", + "ci", + "docs", + "feat", + "fix", + "perf", + "style", + "refactor", + "test" +] +minor_tags = ["feat"] +patch_tags = ["fix", "perf", "refactor", "build", "style"] + +[build-system] +requires = [ + "poetry-core" +] +build-backend = "poetry.core.masonry.api" diff --git a/requirements.txt b/requirements.txt deleted file mode 100644 index 7e9eb3f..0000000 --- a/requirements.txt +++ /dev/null @@ -1,8 +0,0 @@ -torch>=1.0.0 -numpy>=1.16.5 -pandas>=1.0.0 -tqdm>=4.0.0 -scikit-learn>=0.18 -torchvision>=0.7.0 -scikit-survival>=0.15.0 -lifelines>=0.26.4 diff --git a/tests/__init__.py b/tests/__init__.py new file mode 100644 index 0000000..e69de29