diff --git a/.gitignore b/.gitignore new file mode 100644 index 0000000000000000000000000000000000000000..d39052b9f2db2199d69084b80032a37d29bf7cee --- /dev/null +++ b/.gitignore @@ -0,0 +1,42 @@ +.DS_Store +.*env/ +.pyenv*/ +.pytest/ +.python-version +.ipynb_checkpoints/ +.python-version +.coverage_html/ +__pycache__ +.mypy_cache +*.pyc +*.egg-info/ +/data/ +.volumes/ +.pytest_cache/ +.coverage* +htmlcov +try.http +project/ +test_*/ +local/ +target/ +*.swp +*.vscode +.vscode/ +vscode/ +nomad.yaml +gunicorn.log.conf +gunicorn.conf +build/ +dist/ +setup.json +parser.osio.log +gui/src/metainfo.json +gui/src/searchQuantities.json +gui/src/toolkitMetadata.json +gui/src/unitsData.js +examples/workdir/ +gunicorn.log.conf +nomad/gitinfo.py +*/node_modules/ + diff --git a/.gitlab-ci.yml b/.gitlab-ci.yml new file mode 100644 index 0000000000000000000000000000000000000000..d79885bc72c3516de368c054cae7fbe162c74010 --- /dev/null +++ b/.gitlab-ci.yml @@ -0,0 +1,18 @@ +image: python:3.7 + +stages: + - test + +linting: + stage: test + script: + - pip install -e . + - python -m pycodestyle --ignore=E501,E701,E731 north tests + - python -m pylint north tests + - python -m mypy --ignore-missing-imports --follow-imports=silent --no-strict-optional north tests + +tests: + stage: test + script: + - pip install -e . + - python -m pytest --cov=north -sv tests diff --git a/.pylintrc b/.pylintrc new file mode 100644 index 0000000000000000000000000000000000000000..4b96ddc650abee9467b4010c12382677081b5e9f --- /dev/null +++ b/.pylintrc @@ -0,0 +1,813 @@ +[MASTER] + +# 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=pydantic + +# Add files or directories to the blacklist. They should be base names, not +# paths. +ignore=CVS + +# Add files or directories matching the regex patterns to the blacklist. The +# regex matches against base names, not paths. +ignore-patterns= + +# Python code to execute, usually for sys.path manipulation such as +# pygtk.require(). +#init-hook= + +# Use multiple processes to speed up Pylint. Specifying 0 will auto-detect the +# number of processors available to use. +jobs=1 + +# Control the amount of potential inferred values when inferring a single +# object. This can help the performance when dealing with large functions or +# complex, nested conditions. +limit-inference-results=100 + +# List of plugins (as comma separated values of python modules names) to load, +# usually to register additional checkers. +load-plugins= + +# Pickle collected data for later comparisons. +persistent=yes + +# Specify a configuration file. +#rcfile= + +# When enabled, pylint would attempt to guess common misconfiguration and emit +# user-friendly hints instead of false-positive error messages. +suggestion-mode=yes + +# Allow loading of arbitrary C extensions. Extensions are imported into the +# active Python interpreter and may run arbitrary code. +unsafe-load-any-extension=no + + +[MESSAGES CONTROL] + +# Only show warnings with the listed confidence levels. Leave empty to show +# all. Valid levels: HIGH, INFERENCE, INFERENCE_FAILURE, UNDEFINED. +confidence= + +# 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=blacklisted-name, + invalid-name, + missing-docstring, + empty-docstring, + unneeded-not, + singleton-comparison, + misplaced-comparison-constant, + unidiomatic-typecheck, + consider-using-enumerate, + consider-iterating-dictionary, + bad-classmethod-argument, + bad-mcs-method-argument, + bad-mcs-classmethod-argument, + single-string-used-for-slots, + line-too-long, + too-many-lines, + trailing-whitespace, + missing-final-newline, + trailing-newlines, + multiple-statements, + superfluous-parens, + bad-whitespace, + mixed-line-endings, + unexpected-line-ending-format, + bad-continuation, + wrong-spelling-in-comment, + wrong-spelling-in-docstring, + invalid-characters-in-docstring, + multiple-imports, + wrong-import-order, + ungrouped-imports, + wrong-import-position, + useless-import-alias, + old-style-class, + len-as-condition, + raw-checker-failed, + bad-inline-option, + locally-disabled, + locally-enabled, + file-ignored, + suppressed-message, + useless-suppression, + deprecated-pragma, + use-symbolic-message-instead, + c-extension-no-member, + literal-comparison, + comparison-with-itself, + no-self-use, + no-classmethod-decorator, + no-staticmethod-decorator, + useless-object-inheritance, + cyclic-import, + duplicate-code, + too-many-ancestors, + too-many-instance-attributes, + too-few-public-methods, + too-many-public-methods, + too-many-return-statements, + too-many-branches, + too-many-arguments, + too-many-locals, + too-many-statements, + too-many-boolean-expressions, + consider-merging-isinstance, + too-many-nested-blocks, + simplifiable-if-statement, + redefined-argument-from-local, + no-else-return, + consider-using-ternary, + trailing-comma-tuple, + stop-iteration-return, + simplify-boolean-expression, + inconsistent-return-statements, + useless-return, + consider-swap-variables, + consider-using-join, + consider-using-in, + consider-using-get, + chained-comparison, + consider-using-dict-comprehension, + consider-using-set-comprehension, + dangerous-default-value, + pointless-statement, + pointless-string-statement, + expression-not-assigned, + unnecessary-pass, + unnecessary-lambda, + deprecated-lambda, + assign-to-new-keyword, + useless-else-on-loop, + exec-used, + eval-used, + confusing-with-statement, + using-constant-test, + comparison-with-callable, + lost-exception, + assert-on-tuple, + attribute-defined-outside-init, + bad-staticmethod-argument, + protected-access, + arguments-differ, + signature-differs, + abstract-method, + super-init-not-called, + no-init, + non-parent-init-called, + useless-super-delegation, + bad-indentation, + mixed-indentation, + lowercase-l-suffix, + wildcard-import, + deprecated-module, + relative-import, + reimported, + import-self, + misplaced-future, + fixme, + invalid-encoded-data, + global-variable-undefined, + global-statement, + global-at-module-level, + unused-argument, + unused-wildcard-import, + redefined-outer-name, + redefined-builtin, + redefine-in-handler, + undefined-loop-variable, + cell-var-from-loop, + possibly-unused-variable, + self-cls-assignment, + bare-except, + broad-except, + duplicate-except, + try-except-raise, + nonstandard-exception, + raising-format-tuple, + property-on-old-class, + keyword-arg-before-vararg, + logging-not-lazy, + logging-format-interpolation, + logging-fstring-interpolation, + bad-format-string-key, + unused-format-string-key, + missing-format-argument-key, + unused-format-string-argument, + format-combined-specification, + missing-format-attribute, + invalid-format-index, + anomalous-unicode-escape-in-string, + boolean-datetime, + redundant-unittest-assert, + deprecated-method, + bad-thread-instantiation, + shallow-copy-environ, + invalid-envvar-default, + subprocess-popen-preexec-fn, + apply-builtin, + basestring-builtin, + buffer-builtin, + cmp-builtin, + coerce-builtin, + execfile-builtin, + file-builtin, + long-builtin, + raw_input-builtin, + reduce-builtin, + standarderror-builtin, + unicode-builtin, + xrange-builtin, + coerce-method, + delslice-method, + getslice-method, + setslice-method, + no-absolute-import, + old-division, + dict-iter-method, + dict-view-method, + next-method-called, + metaclass-assignment, + indexing-exception, + raising-string, + reload-builtin, + oct-method, + hex-method, + nonzero-method, + cmp-method, + input-builtin, + round-builtin, + intern-builtin, + unichr-builtin, + map-builtin-not-iterating, + zip-builtin-not-iterating, + range-builtin-not-iterating, + filter-builtin-not-iterating, + using-cmp-argument, + eq-without-hash, + div-method, + idiv-method, + rdiv-method, + exception-message-attribute, + invalid-str-codec, + sys-max-int, + bad-python3-import, + deprecated-string-function, + deprecated-str-translate-call, + deprecated-itertools-function, + deprecated-types-field, + next-method-defined, + dict-items-not-iterating, + dict-keys-not-iterating, + dict-values-not-iterating, + deprecated-operator-function, + deprecated-urllib-function, + xreadlines-attribute, + deprecated-sys-function, + exception-escape, + comprehension-escape, + mongoengine-placeholder, + unspecified-encoding + +# 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=syntax-error, + unrecognized-inline-option, + bad-option-value, + init-is-generator, + return-in-init, + function-redefined, + not-in-loop, + return-outside-function, + yield-outside-function, + return-arg-in-generator, + nonexistent-operator, + duplicate-argument-name, + abstract-class-instantiated, + bad-reversed-sequence, + too-many-star-expressions, + invalid-star-assignment-target, + star-needs-assignment-target, + nonlocal-and-global, + continue-in-finally, + nonlocal-without-binding, + used-prior-global-declaration, + misplaced-format-function, + method-hidden, + access-member-before-definition, + no-method-argument, + no-self-argument, + invalid-slots-object, + assigning-non-slot, + invalid-slots, + inherit-non-class, + inconsistent-mro, + duplicate-bases, + non-iterator-returned, + unexpected-special-method-signature, + invalid-length-returned, + import-error, + relative-beyond-top-level, + used-before-assignment, + undefined-variable, + undefined-all-variable, + invalid-all-object, + no-name-in-module, + unbalanced-tuple-unpacking, + unpacking-non-sequence, + bad-except-order, + raising-bad-type, + bad-exception-context, + misplaced-bare-raise, + raising-non-exception, + notimplemented-raised, + catching-non-exception, + slots-on-old-class, + super-on-old-class, + bad-super-call, + missing-super-argument, + no-member, + not-callable, + assignment-from-no-return, + no-value-for-parameter, + too-many-function-args, + unexpected-keyword-arg, + redundant-keyword-arg, + missing-kwoa, + invalid-sequence-index, + invalid-slice-index, + assignment-from-none, + not-context-manager, + invalid-unary-operand-type, + unsupported-binary-operation, + repeated-keyword, + not-an-iterable, + not-a-mapping, + unsupported-membership-test, + unsubscriptable-object, + unsupported-assignment-operation, + unsupported-delete-operation, + invalid-metaclass, + unhashable-dict-key, + logging-unsupported-format, + logging-format-truncated, + logging-too-many-args, + logging-too-few-args, + bad-format-character, + truncated-format-string, + mixed-format-string, + format-needs-mapping, + missing-format-string-key, + too-many-format-args, + too-few-format-args, + bad-str-strip-call, + invalid-envvar-value, + print-statement, + parameter-unpacking, + unpacking-in-except, + old-raise-syntax, + backtick, + long-suffix, + old-ne-operator, + old-octal-literal, + import-star-module-level, + non-ascii-bytes-literal, + yield-inside-async-function, + not-async-context-manager, + fatal, + astroid-error, + parse-error, + method-check-failed, + unreachable, + duplicate-key, + unnecessary-semicolon, + global-variable-not-assigned, + unused-import, + unused-variable, + binary-op-exception, + bad-format-string, + anomalous-backslash-in-string, + bad-open-mode + + +[REPORTS] + +# 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= + +# Set the output format. Available formats are text, parseable, colorized, json +# and msvs (visual studio). You can also give a reporter class, e.g. +# mypackage.mymodule.MyReporterClass. +output-format=text + +# Tells whether to display a full report or only the messages. +reports=no + +# Activate the evaluation score. +score=yes + + +[REFACTORING] + +# Maximum number of nested blocks for function / method body +max-nested-blocks=5 + +# Complete name of functions that never returns. When checking for +# inconsistent-return-statements if a never returning function is called then +# it will be considered as an explicit return statement and no message will be +# printed. +never-returning-functions=sys.exit + + +[BASIC] + +# Naming style matching correct argument names. +argument-naming-style=snake_case + +# Regular expression matching correct argument names. Overrides argument- +# naming-style. +#argument-rgx= + +# Naming style matching correct attribute names. +attr-naming-style=snake_case + +# Regular expression matching correct attribute names. Overrides attr-naming- +# style. +#attr-rgx= + +# Bad variable names which should always be refused, separated by a comma. +bad-names=foo, + bar, + baz, + toto, + tutu, + tata + +# Naming style matching correct class attribute names. +class-attribute-naming-style=any + +# Regular expression matching correct class attribute names. Overrides class- +# attribute-naming-style. +#class-attribute-rgx= + +# Naming style matching correct class names. +class-naming-style=PascalCase + +# Regular expression matching correct class names. Overrides class-naming- +# style. +#class-rgx= + +# Naming style matching correct constant names. +const-naming-style=UPPER_CASE + +# Regular expression matching correct constant names. Overrides const-naming- +# style. +#const-rgx= + +# Minimum line length for functions/classes that require docstrings, shorter +# ones are exempt. +docstring-min-length=-1 + +# Naming style matching correct function names. +function-naming-style=snake_case + +# Regular expression matching correct function names. Overrides function- +# naming-style. +#function-rgx= + +# Good variable names which should always be accepted, separated by a comma. +good-names=i, + j, + k, + ex, + Run, + _ + +# Include a hint for the correct naming format with invalid-name. +include-naming-hint=no + +# Naming style matching correct inline iteration names. +inlinevar-naming-style=any + +# Regular expression matching correct inline iteration names. Overrides +# inlinevar-naming-style. +#inlinevar-rgx= + +# Naming style matching correct method names. +method-naming-style=snake_case + +# Regular expression matching correct method names. Overrides method-naming- +# style. +#method-rgx= + +# Naming style matching correct module names. +module-naming-style=snake_case + +# Regular expression matching correct module names. Overrides module-naming- +# style. +#module-rgx= + +# Colon-delimited sets of names that determine each other's naming style when +# the name regexes allow several styles. +name-group= + +# Regular expression which should only match function or class names that do +# not require a docstring. +no-docstring-rgx=^_ + +# List of decorators that produce properties, such as abc.abstractproperty. Add +# to this list to register other decorators that produce valid properties. +# These decorators are taken in consideration only for invalid-name. +property-classes=abc.abstractproperty + +# Naming style matching correct variable names. +variable-naming-style=snake_case + +# Regular expression matching correct variable names. Overrides variable- +# naming-style. +#variable-rgx= + + +[FORMAT] + +# Expected format of line ending, e.g. empty (any line ending), LF or CRLF. +expected-line-ending-format= + +# Regexp for a line that is allowed to be longer than the limit. +ignore-long-lines=^\s*(# )?<?https?://\S+>?$ + +# Number of spaces of indent required inside a hanging or continued line. +indent-after-paren=4 + +# String used as indentation unit. This is usually " " (4 spaces) or "\t" (1 +# tab). +indent-string=' ' + +# Maximum number of characters on a single line. +max-line-length=100 + +# Maximum number of lines in a module. +max-module-lines=1000 + +# 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=trailing-comma, + dict-separator + +# Allow the body of a class to be on the same line as the declaration if body +# contains single statement. +single-line-class-stmt=no + +# Allow the body of an if to be on the same line as the test if there is no +# else. +single-line-if-stmt=no + + +[LOGGING] + +# Logging modules to check that the string format arguments are in logging +# function parameter format. +logging-modules=logging + + +[MISCELLANEOUS] + +# List of note tags to take in consideration, separated by a comma. +notes=FIXME, + XXX, + TODO + + +[SIMILARITIES] + +# Ignore comments when computing similarities. +ignore-comments=yes + +# Ignore docstrings when computing similarities. +ignore-docstrings=yes + +# Ignore imports when computing similarities. +ignore-imports=no + +# Minimum lines number of a similarity. +min-similarity-lines=4 + + +[SPELLING] + +# Limits count of emitted suggestions for spelling mistakes. +max-spelling-suggestions=4 + +# 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 + + +[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 + +# 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= + +# 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 + +# Tells whether to warn about missing members when the owner of the attribute +# is inferred to be None. +ignore-none=yes + +# This flag controls whether pylint should warn about no-member and similar +# checks whenever an opaque object is returned when inferring. The inference +# can return multiple potential results while evaluating a Python object, but +# some branches might not be evaluated, which results in partial inference. In +# that case, it might be useful to still emit no-member and other checks for +# the rest of the inferred objects. +ignore-on-opaque-inference=yes + +# 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,SearchResponse + +# 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= + +# Show a hint with possible names when a member name was not found. The aspect +# of finding the hint is based on edit distance. +missing-member-hint=yes + +# The minimum edit distance a name should have in order to be considered a +# similar match for a missing member name. +missing-member-hint-distance=1 + +# The total number of similar names that should be taken in consideration when +# showing a hint for a missing member. +missing-member-max-choices=1 + + +[VARIABLES] + +# List of additional names supposed to be defined in builtins. Remember that +# you should avoid to define new builtins when possible. +additional-builtins= + +# Tells whether unused global variables should be treated as a violation. +allow-global-unused-variables=yes + +# 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 + +# A regular expression matching the name of dummy variables (i.e. expected to +# not be used). +dummy-variables-rgx=_+$|(_[a-zA-Z0-9_]*[a-zA-Z0-9]+?$)|dummy|^ignored_|^unused_ + +# Argument names that match this expression will be ignored. Default to name +# with leading underscore. +ignored-argument-names=_.*|^ignored_|^unused_ + +# Tells whether we should check for unused import in __init__ files. +init-import=no + +# List of qualified module names which can have objects that can redefine +# builtins. +redefining-builtins-modules=six.moves,past.builtins,future.builtins,builtins,io + + +[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 + +# List of valid names for the first argument in a metaclass class method. +valid-metaclass-classmethod-first-arg=cls + + +[DESIGN] + +# Maximum number of arguments for function / method. +max-args=5 + +# Maximum number of attributes for a class (see R0902). +max-attributes=7 + +# Maximum number of boolean expressions in an if statement. +max-bool-expr=5 + +# Maximum number of branch for function / method body. +max-branches=12 + +# Maximum number of locals for function / method body. +max-locals=15 + +# Maximum number of parents for a class (see R0901). +max-parents=7 + +# Maximum number of public methods for a class (see R0904). +max-public-methods=20 + +# Maximum number of return / yield for function / method body. +max-returns=6 + +# Maximum number of statements in function / method body. +max-statements=50 + +# Minimum number of public methods for a class (see R0903). +min-public-methods=2 + + +[IMPORTS] + +# Allow wildcard imports from modules that define __all__. +allow-wildcard-with-all=no + +# 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 + +# Deprecated modules which should not be used, separated by a comma. +deprecated-modules=optparse,tkinter.tix + +# Create a graph of external dependencies in the given file (report RP0402 must +# not be disabled). +ext-import-graph= + +# 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 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 + + +[EXCEPTIONS] + +# Exceptions that will emit a warning when being caught. Defaults to +# "Exception". +overgeneral-exceptions=Exception diff --git a/AUTHORS b/AUTHORS new file mode 100644 index 0000000000000000000000000000000000000000..2ee9f19a2b60e03be8c464aaa202472d5b766d54 --- /dev/null +++ b/AUTHORS @@ -0,0 +1,2 @@ +Markus Scheidgen <markus.scheidgen@gmail.com> +TODO developers add yourself diff --git a/MANIFEST.in b/MANIFEST.in new file mode 100644 index 0000000000000000000000000000000000000000..c1d53f41fa7732b912d85974d8ef6ad543f8518d --- /dev/null +++ b/MANIFEST.in @@ -0,0 +1,9 @@ +recursive-include dependencies/optimade-python-tools *.txt *.g *.py *.ini *.json +recursive-include nomad *.json *.j2 *.md *.yaml +include nomad/units/*.txt +include README.md +include LICENSE.txt +include requirements.txt +include auto_complete_install.sh +include setup.json +recursive-include nomad/app/static *.css *.ico *.html *.json *.js *.map *.txt *.svg *.png \ No newline at end of file diff --git a/README.md b/README.md index fcdbef7dee8000409d7e51b769ba95debc92cbae..407fe385f993ecb8a60952fac91710a9d4d5c33a 100644 --- a/README.md +++ b/README.md @@ -1,4 +1,68 @@ +[](https://gitlab.mpcdf.mpg.de/nomad-lab/nomad-remote-tools-hub/commits/main) +[](https://gitlab.mpcdf.mpg.de/nomad-lab/nomad-remote-tools-hub/commits/main) + # NOMAD remote tools hub (north) Lets you run containarized tools remotly. +## Getting started + +Clone the project + +```sh +git clone git@gitlab.mpcdf.mpg.de:nomad-lab/nomad-remote-tools-hub.git +cd nomad-remote-tools-hub +``` + +Optionaly, checkout the desired branch (e.g. develop) and create a feature branch +``` +git checkout develop +git checkout -b my-feature +``` + +Create a virtual environment based on Python 3 (>3.7). +```sh +pip install virtualenv +virtualenv -p `which python3` .pyenv +source .pyenv/bin/activate +``` + +Install the nomad-remote-tools-hub package. +```sh +pip install -e . +``` + +Run the app with uvivcorn: +```sh +uvicorn north.app.main:app +``` + +Run the tests with pytest: +```sh +pytest -svx test +``` + +We recomment using vs-code. Here are vs-code settings that match the CI/CD linting: +```json +{ + "python.pythonPath": ".pyenv/bin/python", + "editor.rulers": [90], + "editor.renderWhitespace": "all", + "editor.tabSize": 4, + "files.trimTrailingWhitespace": true, + "python.linting.pycodestylePath": "pycodestyle", + "python.linting.pycodestyleEnabled": true, + "python.linting.pycodestyleArgs": ["--ignore=E501,E701,E731"], + "python.linting.mypyEnabled": true, + "python.linting.pylintEnabled": true, +} +``` + +## Project structure + +- `north` - The Python code +- `north/app` - The [FastAPI](https://fastapi.tiangolo.com/) application that runs the north app +- `north/config` - All applications settings +- `tests` - The [pytest](https://docs.pytest.org/) tests +- `setup.py` - Install the package with pip +- `docker` - All the docker files, scripts for creating/managing images, documentation diff --git a/docker/README.md b/docker/README.md new file mode 100644 index 0000000000000000000000000000000000000000..8e227aef516decaaeee63840be63da51abbeb423 --- /dev/null +++ b/docker/README.md @@ -0,0 +1,4 @@ +**TODO** This directory should contain the docker files and image documentation +- one folder per "tool" +- also for images necessary for tests (e.g. nginx with static rev.proxy rules) +- scripts to create images and push them to the projects registry \ No newline at end of file diff --git a/north/__init__.py b/north/__init__.py new file mode 100644 index 0000000000000000000000000000000000000000..7732f327207b056e58ef63290c43033a08ab2f62 --- /dev/null +++ b/north/__init__.py @@ -0,0 +1,19 @@ +# +# Copyright The NOMAD Authors. +# +# This file is part of NOMAD. See https://nomad-lab.eu for further info. +# +# 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 +# +# http://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. +# + +from .config import config diff --git a/north/app/__init__.py b/north/app/__init__.py new file mode 100644 index 0000000000000000000000000000000000000000..e69de29bb2d1d6434b8b29ae775ad8c2e48c5391 diff --git a/north/app/main.py b/north/app/main.py new file mode 100644 index 0000000000000000000000000000000000000000..cdba8ead14d7f7cb2c8d7a7f3afdd618cb91a8ec --- /dev/null +++ b/north/app/main.py @@ -0,0 +1,61 @@ +# +# Copyright The NOMAD Authors. +# +# This file is part of NOMAD. See https://nomad-lab.eu for further info. +# +# 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 +# +# http://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. +# + +from fastapi import FastAPI +from fastapi.responses import HTMLResponse +from starlette.exceptions import HTTPException as StarletteHTTPException +from fastapi.exception_handlers import http_exception_handler as default_http_exception_handler + +from north import config + +from .routes import instances +from .routes import tools + +app = FastAPI( + title='NOMAD remote tools hub API', + version=config.version, + description=( + 'This is the API for the NOMAD remote tools hub. It allows to run dockerized ' + 'tools remotely.')) + +app.include_router(tools.router, prefix='/tools') +app.include_router(instances.router, prefix='/instances') + + +# A default 404 response with a link to the API dashboard for convinience +@app.exception_handler(StarletteHTTPException) +async def http_exception_handler(request, exc): + if exc.status_code != 404: + return await default_http_exception_handler(request, exc) + + try: + accept = request.headers['accept'] + except Exception: + accept = None + + if accept is not None and 'html' in accept: + return HTMLResponse(status_code=404, content=''' + <html> + <head><title>NOMAD remote tools hub app</title></head> + <body> + <h1>NOMAD remote tools hub app</h1> + <h2>apis</h2> + <a href="/docs">OpenAPI dashboard</a> + </body> + </html> + ''') diff --git a/north/app/models.py b/north/app/models.py new file mode 100644 index 0000000000000000000000000000000000000000..eca8c02e28d2a929072ab1303e820632bd3972fe --- /dev/null +++ b/north/app/models.py @@ -0,0 +1,57 @@ +# +# Copyright The NOMAD Authors. +# +# This file is part of NOMAD. See https://nomad-lab.eu for further info. +# +# 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 +# +# http://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. +# + +from typing import List, Dict, Optional +from pydantic import BaseModel, validator, Field + +# TODO This exemplifies pydantic models a little bit. But, this is just for demonstration. +# The models completed/rewritten and most descriptions are missing. + + +class ToolModel(BaseModel): + ''' Model that describes an available tool. ''' + name: str + description: str + docker_image: str = Field(..., description='The docker image for this tool.') + + +all_tools: List[ToolModel] = [ + ToolModel( + name='jupyter', + description='Basic jupyter run with an empty notebook or on given notebook file.', + docker_image='TODO' + ), + ToolModel( + name='hyperspy', + description='Run hyperspy on a arbitrary .hdf5 file.', + docker_image='TODO' + ) +] + +tools_map: Dict[str, ToolModel] = {tool.name: tool for tool in all_tools} + + +class InstanceModel(BaseModel): + name: str + docker_id: Optional[str] + tool_name: str + + @validator('tool_name') + def validate_tool_name(cls, tool_name): # pylint: disable=no-self-argument + assert tool_name in tools_map, 'Tool must exist.' + return tool_name diff --git a/north/app/routes/instances.py b/north/app/routes/instances.py new file mode 100644 index 0000000000000000000000000000000000000000..a3b8a3550ef43c4e63795249db64f4434661dfe4 --- /dev/null +++ b/north/app/routes/instances.py @@ -0,0 +1,47 @@ +# +# Copyright The NOMAD Authors. +# +# This file is part of NOMAD. See https://nomad-lab.eu for further info. +# +# 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 +# +# http://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. +# + +from typing import List +from fastapi import APIRouter + +from north.app.models import InstanceModel + +router = APIRouter() +router_tag = 'instances' + + +@router.get( + '/', + tags=[router_tag], + response_model=List[InstanceModel], + response_model_exclude_unset=True, + response_model_exclude_none=True) +async def get_instances(): + ''' Get a list of all existing tool instances. ''' + return [] + + +@router.post( + '/', + tags=[router_tag], + response_model=InstanceModel, + response_model_exclude_unset=True, + response_model_exclude_none=True) +async def post_instances(instance: InstanceModel): + ''' Create a new tool instance. ''' + return instance diff --git a/north/app/routes/tools.py b/north/app/routes/tools.py new file mode 100644 index 0000000000000000000000000000000000000000..b54c1d2a26feb959639e0133348b47393d248bb3 --- /dev/null +++ b/north/app/routes/tools.py @@ -0,0 +1,35 @@ +# +# Copyright The NOMAD Authors. +# +# This file is part of NOMAD. See https://nomad-lab.eu for further info. +# +# 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 +# +# http://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. +# + +from typing import List +from fastapi import APIRouter + +from north.app.models import ToolModel, all_tools + +router = APIRouter() +router_tag = 'tools' + + +@router.get( + '/', + tags=[router_tag], + response_model=List[ToolModel], + response_model_exclude_unset=True, + response_model_exclude_none=True) +async def get_tools(): + return all_tools diff --git a/north/config.py b/north/config.py new file mode 100644 index 0000000000000000000000000000000000000000..c4d22eba8f3445d9b11f1bba1da64703cbb61b42 --- /dev/null +++ b/north/config.py @@ -0,0 +1,70 @@ +# +# Copyright The NOMAD Authors. +# +# This file is part of NOMAD. See https://nomad-lab.eu for further info. +# +# 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 +# +# http://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. +# + +''' +This config file is based on pydantic's +[settings management](https://pydantic-docs.helpmanual.io/usage/settings/). +''' + +from typing import Dict, Any +from pydantic import Field, BaseSettings +import yaml +import os.path +import os + + +class NorthConfig(BaseSettings): + secret: str = Field( + 'this is a secret', + description='The secret for generating JWT tokens and other cryptographic material.') + + version: str = Field( + 'v0.1.0', description='The current application version according to semantic versioning conventions') + + class Config: + env_prefix = 'north_' + case_sensitive = False + + @classmethod + def customise_sources( + cls, + init_settings, + env_settings, + file_secret_settings): + + return ( + init_settings, + env_settings, + yaml_config_settings_source, file_secret_settings) + + +def yaml_config_settings_source(settings: BaseSettings) -> Dict[str, Any]: + if not os.path.exists('north.yaml'): + return {} + + try: + with open('north.yaml') as f: + data = yaml.load(f, Loader=yaml.FullLoader) + if data is None: + return {} + return data + except yaml.YAMLError as e: + raise e + + +config = NorthConfig() diff --git a/requirements.txt b/requirements.txt new file mode 100644 index 0000000000000000000000000000000000000000..464e64af096873e00b23f5b97b6bbb7f5a69852e --- /dev/null +++ b/requirements.txt @@ -0,0 +1,11 @@ +pyyaml +fastapi +requests +setuptools +mypy +pylint +pycodestyle +pytest +pytest-cov +types-PyYAML +types-requests diff --git a/setup.py b/setup.py new file mode 100644 index 0000000000000000000000000000000000000000..fca1381d70e1a78ad5d70e7d5632bc92696fa65b --- /dev/null +++ b/setup.py @@ -0,0 +1,38 @@ +# +# Copyright The NOMAD Authors. +# +# This file is part of NOMAD. See https://nomad-lab.eu for further info. +# +# 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 +# +# http://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. +# + +from setuptools import setup, find_packages + + +with open('requirements.txt') as f: + requirements = f.read().splitlines() + + +def main(): + setup( + name='nomad-remote-tools-hub', + version='0.1.0', + description='NOMAD remote tools hub allows to run containarized tools remotely', + author='The NOMAD Authors', + license='APACHE 2.0', + packages=find_packages(exclude=['tests', 'tests.*']), + install_requires=requirements) + + +if __name__ == '__main__': + main() diff --git a/tests/__init__.py b/tests/__init__.py new file mode 100644 index 0000000000000000000000000000000000000000..db96892bc39fc672a63d1827096f3e0fcf7a818c --- /dev/null +++ b/tests/__init__.py @@ -0,0 +1,17 @@ +# +# Copyright The NOMAD Authors. +# +# This file is part of NOMAD. See https://nomad-lab.eu for further info. +# +# 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 +# +# http://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/tests/app/__init__.py b/tests/app/__init__.py new file mode 100644 index 0000000000000000000000000000000000000000..db96892bc39fc672a63d1827096f3e0fcf7a818c --- /dev/null +++ b/tests/app/__init__.py @@ -0,0 +1,17 @@ +# +# Copyright The NOMAD Authors. +# +# This file is part of NOMAD. See https://nomad-lab.eu for further info. +# +# 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 +# +# http://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/tests/app/routes/__init__.py b/tests/app/routes/__init__.py new file mode 100644 index 0000000000000000000000000000000000000000..db96892bc39fc672a63d1827096f3e0fcf7a818c --- /dev/null +++ b/tests/app/routes/__init__.py @@ -0,0 +1,17 @@ +# +# Copyright The NOMAD Authors. +# +# This file is part of NOMAD. See https://nomad-lab.eu for further info. +# +# 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 +# +# http://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/tests/app/routes/test_instance.py b/tests/app/routes/test_instance.py new file mode 100644 index 0000000000000000000000000000000000000000..65573fd54af17fc43c7cbd8521ecb9f4540c4125 --- /dev/null +++ b/tests/app/routes/test_instance.py @@ -0,0 +1,35 @@ +# +# Copyright The NOMAD Authors. +# +# This file is part of NOMAD. See https://nomad-lab.eu for further info. +# +# 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 +# +# http://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. +# + +import pytest + + +def test_get_instances(api): + response = api.get('instances') + assert response.status_code == 200, response.text + assert len(response.json()) == 0 + + +@pytest.mark.parametrize('request_json, status_code', [ + pytest.param({'name': 'myinstance', 'tool_name': 'jupyter'}, 200, id='ok'), + pytest.param({'name': 'myinstance', 'tool_name': 'doesnotexist'}, 422, id='tool-does-not-exist'), + pytest.param({'tool_name': 'jupyter'}, 422, id='name-is-missing') +]) +def test_post_instances(api, request_json, status_code): + response = api.post('instances/', json=request_json) + assert response.status_code == status_code, response.text diff --git a/tests/app/routes/test_tools.py b/tests/app/routes/test_tools.py new file mode 100644 index 0000000000000000000000000000000000000000..293ea8f19d37c132797dd1338dae4959ccfad5ad --- /dev/null +++ b/tests/app/routes/test_tools.py @@ -0,0 +1,25 @@ +# +# Copyright The NOMAD Authors. +# +# This file is part of NOMAD. See https://nomad-lab.eu for further info. +# +# 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 +# +# http://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. +# + +from north.app.models import all_tools + + +def test_get_tools(api): + response = api.get('tools') + assert response.status_code == 200, response.text + assert len(response.json()) == len(all_tools) diff --git a/tests/conftest.py b/tests/conftest.py new file mode 100644 index 0000000000000000000000000000000000000000..1d07377523fa717988e041606c54b890fc8c1d73 --- /dev/null +++ b/tests/conftest.py @@ -0,0 +1,32 @@ +# +# Copyright The NOMAD Authors. +# +# This file is part of NOMAD. See https://nomad-lab.eu for further info. +# +# 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 +# +# http://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. +# + +import pytest +from fastapi.testclient import TestClient + +from north.app.main import app + + +@pytest.fixture(scope='session') +def api(): + ''' + This fixture provides an HTTP client with Python requests interface that accesses + the api. + ''' + test_client = TestClient(app, base_url='http://testserver') + return test_client diff --git a/tests/pytest.ini b/tests/pytest.ini new file mode 100644 index 0000000000000000000000000000000000000000..b0e5a945f5415a31f1161ea8fb6f09d1f35ff33b --- /dev/null +++ b/tests/pytest.ini @@ -0,0 +1,3 @@ +[pytest] +filterwarnings = + ignore::DeprecationWarning \ No newline at end of file