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+backend/shared-modules + +# IDE files +.idea diff --git a/.gitmodules b/.gitmodules index bfd7d7024..c5d308bb2 100644 --- a/.gitmodules +++ b/.gitmodules @@ -1,9 +1,6 @@ [submodule "deps/sadisplay"] path = deps/sadisplay url = https://github.com/davenquinn/sadisplay.git -[submodule "backend/python-tools"] - path = backend/shared-modules - url = https://github.com/UW-Macrostrat/python-tools.git [submodule "deps/postgis-tile-utils"] path = backend/deps/postgis-tile-utils url = https://github.com/UW-Macrostrat/postgis-tile-utils.git diff --git a/_cli/poetry.lock b/_cli/poetry.lock index a482de4e6..fcf3d5f10 100644 --- a/_cli/poetry.lock +++ b/_cli/poetry.lock @@ -1,25 +1,36 @@ -# This file is automatically @generated by Poetry 1.6.1 and should not be changed by hand. +# This file is automatically @generated by Poetry 1.8.2 and should not be changed by hand. + +[[package]] +name = "aiofiles" +version = "23.2.1" +description = "File support for asyncio." +optional = false +python-versions 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"sha256:85cf3842da2bf060760f955f8467b87983fb2e30f1764fd0e24a48307dc8ec6e"}, ] [package.dependencies] -six = "*" -SQLAlchemy = ">=1.0" +SQLAlchemy = ">=1.3" [package.extras] arrow = ["arrow (>=0.3.4)"] @@ -819,8 +854,8 @@ intervals = ["intervals (>=0.7.1)"] password = ["passlib (>=1.6,<2.0)"] pendulum = ["pendulum (>=2.0.5)"] phone = ["phonenumbers (>=5.9.2)"] -test = ["Jinja2 (>=2.3)", "Pygments (>=1.2)", "backports.zoneinfo", "docutils (>=0.10)", "flake8 (>=2.4.0)", "flexmock (>=0.9.7)", "isort (>=4.2.2)", "mock (==2.0.0)", "pg8000 (>=1.12.4)", "psycopg2 (>=2.5.1)", "psycopg2cffi (>=2.8.1)", "pymysql", "pyodbc", "pytest (>=2.7.1)", "python-dateutil (>=2.6)", "pytz (>=2014.2)"] -test-all = ["Babel (>=1.3)", "Jinja2 (>=2.3)", "Pygments (>=1.2)", "arrow (>=0.3.4)", "backports.zoneinfo", "colour (>=0.0.4)", "cryptography (>=0.6)", "docutils (>=0.10)", "flake8 (>=2.4.0)", "flexmock (>=0.9.7)", "furl (>=0.4.1)", "intervals (>=0.7.1)", "isort (>=4.2.2)", "mock (==2.0.0)", "passlib (>=1.6,<2.0)", "pendulum (>=2.0.5)", "pg8000 (>=1.12.4)", "phonenumbers (>=5.9.2)", "psycopg2 (>=2.5.1)", "psycopg2cffi (>=2.8.1)", "pymysql", "pyodbc", "pytest (>=2.7.1)", "python-dateutil", "python-dateutil (>=2.6)", "pytz (>=2014.2)"] +test = ["Jinja2 (>=2.3)", "Pygments (>=1.2)", "backports.zoneinfo", "docutils (>=0.10)", "flake8 (>=2.4.0)", "flexmock (>=0.9.7)", "isort (>=4.2.2)", "pg8000 (>=1.12.4)", "psycopg (>=3.1.8)", "psycopg2 (>=2.5.1)", "psycopg2cffi (>=2.8.1)", "pymysql", "pyodbc", "pytest (==7.4.4)", "python-dateutil (>=2.6)", "pytz (>=2014.2)"] +test-all = ["Babel (>=1.3)", "Jinja2 (>=2.3)", "Pygments (>=1.2)", "arrow (>=0.3.4)", "backports.zoneinfo", "colour (>=0.0.4)", "cryptography (>=0.6)", "docutils (>=0.10)", "flake8 (>=2.4.0)", "flexmock (>=0.9.7)", "furl (>=0.4.1)", "intervals (>=0.7.1)", "isort (>=4.2.2)", "passlib (>=1.6,<2.0)", "pendulum (>=2.0.5)", "pg8000 (>=1.12.4)", "phonenumbers (>=5.9.2)", "psycopg (>=3.1.8)", "psycopg2 (>=2.5.1)", "psycopg2cffi (>=2.8.1)", "pymysql", "pyodbc", "pytest (==7.4.4)", "python-dateutil", "python-dateutil (>=2.6)", "pytz (>=2014.2)"] timezone = ["python-dateutil"] url = ["furl (>=0.4.1)"] @@ -874,46 +909,33 @@ files = [ [[package]] name = "typing-extensions" -version = "4.9.0" +version = "4.12.2" description = "Backported and Experimental Type Hints for Python 3.8+" optional = false python-versions = ">=3.8" files = [ - {file = "typing_extensions-4.9.0-py3-none-any.whl", hash = "sha256:af72aea155e91adfc61c3ae9e0e342dbc0cba726d6cba4b6c72c1f34e47291cd"}, - {file = "typing_extensions-4.9.0.tar.gz", hash = "sha256:23478f88c37f27d76ac8aee6c905017a143b0b1b886c3c9f66bc2fd94f9f5783"}, + {file = "typing_extensions-4.12.2-py3-none-any.whl", hash = "sha256:04e5ca0351e0f3f85c6853954072df659d0d13fac324d0072316b67d7794700d"}, + {file = "typing_extensions-4.12.2.tar.gz", hash = "sha256:1a7ead55c7e559dd4dee8856e3a88b41225abfe1ce8df57b7c13915fe121ffb8"}, ] [[package]] name = "urllib3" -version = "1.26.15" +version = "2.2.2" description = "HTTP library with thread-safe connection pooling, file post, and more." optional = false -python-versions = ">=2.7, !=3.0.*, !=3.1.*, !=3.2.*, !=3.3.*, !=3.4.*, !=3.5.*" +python-versions = ">=3.8" files = [ - {file = "urllib3-1.26.15-py2.py3-none-any.whl", hash = "sha256:aa751d169e23c7479ce47a0cb0da579e3ede798f994f5816a74e4f4500dcea42"}, - {file = "urllib3-1.26.15.tar.gz", hash = "sha256:8a388717b9476f934a21484e8c8e61875ab60644d29b9b39e11e4b9dc1c6b305"}, + {file = "urllib3-2.2.2-py3-none-any.whl", hash = "sha256:a448b2f64d686155468037e1ace9f2d2199776e17f0a46610480d311f73e3472"}, + {file = "urllib3-2.2.2.tar.gz", hash = "sha256:dd505485549a7a552833da5e6063639d0d177c04f23bc3864e41e5dc5f612168"}, ] [package.extras] -brotli = ["brotli (>=1.0.9)", "brotlicffi (>=0.8.0)", "brotlipy (>=0.6.0)"] -secure = ["certifi", "cryptography (>=1.3.4)", "idna (>=2.0.0)", "ipaddress", "pyOpenSSL (>=0.14)", "urllib3-secure-extra"] -socks = ["PySocks (>=1.5.6,!=1.5.7,<2.0)"] - -[[package]] -name = "websocket-client" -version = "0.59.0" -description = "WebSocket client for Python with low level API options" -optional = false -python-versions = ">=2.6, !=3.0.*, !=3.1.*, !=3.2.*, !=3.3.*" -files = [ - {file = "websocket-client-0.59.0.tar.gz", hash = "sha256:d376bd60eace9d437ab6d7ee16f4ab4e821c9dae591e1b783c58ebd8aaf80c5c"}, - {file = "websocket_client-0.59.0-py2.py3-none-any.whl", hash = "sha256:2e50d26ca593f70aba7b13a489435ef88b8fc3b5c5643c1ce8808ff9b40f0b32"}, -] - -[package.dependencies] -six = "*" +brotli = ["brotli (>=1.0.9)", "brotlicffi (>=0.8.0)"] +h2 = ["h2 (>=4,<5)"] +socks = ["pysocks (>=1.5.6,!=1.5.7,<2.0)"] +zstd = ["zstandard (>=0.18.0)"] [metadata] lock-version = "2.0" python-versions = "^3.8" -content-hash = "4cc54966a354094dca08335ecd2e297459eed19db986653f8276383a1f6d27b8" +content-hash = "e684c5ea430e659f8ec97707355979f66fa771aee88c416e2728883aa4e8c07f" diff --git a/_cli/pyproject.toml b/_cli/pyproject.toml index 99eb993d9..cf3e30006 100644 --- a/_cli/pyproject.toml +++ b/_cli/pyproject.toml @@ -16,21 +16,18 @@ envbash = "*" pytest = "*" pyyaml = "^6.0.1" pydantic = "^1.9.0" -# The below pin of 'docker' ensures that we don't encounter -# https://github.com/docker/compose/issues/8499 -# It should be deleted when docker-compose dependency is upgraded. -docker = "^6.0.1" +docker = "^7.1.0" click-default-group = "^1.2.2" keepachangelog = "2.0.0.dev2" packaging = "^23.2" # Utility functions (we would move this to a separate folder, ideally) -"macrostrat.utils" = { path = "../backend/shared-modules/utils", develop = true } +"macrostrat.utils" = "^1.2.1" # Database backup and schema migration functionality -"macrostrat.dinosaur" = {path = "../backend/shared-modules/dinosaur", develop = true } -"macrostrat.database" = {path = "../backend/shared-modules/database", develop = true } +"macrostrat.dinosaur" = "^3.1.0" +"macrostrat.database" = "^3.3.1" chardet = "^5.1.0" charset-normalizer = "2.1.0" @@ -41,4 +38,4 @@ sparrow = "sparrow_cli:cli" [tool.black] line-length = 88 skip-magic-trailing-comma = true -target-version = ['py38'] \ No newline at end of file +target-version = ['py38'] diff --git a/backend/Dockerfile b/backend/Dockerfile index ec514efb7..27a0ab78d 100644 --- a/backend/Dockerfile +++ b/backend/Dockerfile @@ -12,11 +12,6 @@ WORKDIR /app # For shared modules, first copy only requirements to install their dependencies. # Poetry must see them as a set of modules. COPY poetry.lock pyproject.toml /app/ -COPY __docker/dummy-shared-module-tree /app/shared-modules -COPY shared-modules/database/pyproject.toml /app/shared-modules/database/ -COPY shared-modules/dinosaur/pyproject.toml /app/shared-modules/dinosaur/ -COPY shared-modules/utils/pyproject.toml /app/shared-modules/utils/ -COPY shared-modules/pyproject.toml /app/shared-modules/pyproject.toml RUN mkdir -p /app/loader/sparrow/loader && touch /app/loader/sparrow/loader/__init__.py COPY loader/pyproject.toml /app/loader/ @@ -42,7 +37,7 @@ COPY ./docker-scripts/* /bin/ ## Copy app core COPY ./ /app/ -RUN poetry install --no-interaction --no-ansi +RUN poetry install --no-interaction --no-ansi # Copy command-line options to a place where they can be easily accessed # by the wrapper CLI. diff --git a/backend/__docker/dummy-shared-module-tree/database/macrostrat/database/__init__.py b/backend/__docker/dummy-shared-module-tree/database/macrostrat/database/__init__.py deleted file mode 100644 index e69de29bb..000000000 diff --git a/backend/__docker/dummy-shared-module-tree/dinosaur/macrostrat/dinosaur/__init__.py b/backend/__docker/dummy-shared-module-tree/dinosaur/macrostrat/dinosaur/__init__.py deleted file mode 100644 index e69de29bb..000000000 diff --git a/backend/__docker/dummy-shared-module-tree/utils/macrostrat/utils/__init__.py b/backend/__docker/dummy-shared-module-tree/utils/macrostrat/utils/__init__.py deleted file mode 100644 index e69de29bb..000000000 diff --git a/backend/loader/pyproject.toml b/backend/loader/pyproject.toml index 144452f8e..48ca6f9f0 100644 --- a/backend/loader/pyproject.toml +++ b/backend/loader/pyproject.toml @@ -13,13 +13,11 @@ python = "^3.9" marshmallow = "^3.20.1" marshmallow-sqlalchemy = "^0.29.0" marshmallow-jsonschema = "^0.13.0" -GeoAlchemy2 = "^0.9.4" -SQLAlchemy = "^1.4.41" -"macrostrat.database" = "^2.0.1" +"macrostrat.database" = "^3.3.1" stringcase = "^1.2.0" shapely = "^1" typer = "^0.6.1" -rich = "^12.6.0" +rich = "^13" [tool.poetry.group.dev.dependencies] pytest = "^7.1.3" diff --git a/backend/poetry.lock b/backend/poetry.lock index 60b9ed491..9d2c42d0b 100644 --- a/backend/poetry.lock +++ b/backend/poetry.lock @@ -1,95 +1,88 @@ -# This file is automatically @generated by Poetry 1.4.2 and should not be changed by hand. +# This file is automatically @generated by Poetry 1.8.2 and should not be changed by hand. [[package]] name = "aiofiles" -version = "0.6.0" +version = "23.2.1" description = "File support for asyncio." -category = "main" optional = false -python-versions = "*" +python-versions = ">=3.7" files = [ - {file = "aiofiles-0.6.0-py3-none-any.whl", hash = "sha256:bd3019af67f83b739f8e4053c6c0512a7f545b9a8d91aaeab55e6e0f9d123c27"}, - {file = "aiofiles-0.6.0.tar.gz", hash = "sha256:e0281b157d3d5d59d803e3f4557dcc9a3dff28a4dd4829a9ff478adae50ca092"}, + {file = "aiofiles-23.2.1-py3-none-any.whl", hash = "sha256:19297512c647d4b27a2cf7c34caa7e405c0d60b5560618a29a9fe027b18b0107"}, + {file = "aiofiles-23.2.1.tar.gz", hash = "sha256:84ec2218d8419404abcb9f0c02df3f34c6e0a68ed41072acfb1cef5cbc29051a"}, ] [[package]] name = "amqp" -version = "5.1.1" +version = "5.2.0" description = "Low-level AMQP client for Python (fork of amqplib)." -category = "main" optional = false python-versions = ">=3.6" files = [ - {file = "amqp-5.1.1-py3-none-any.whl", hash = "sha256:6f0956d2c23d8fa6e7691934d8c3930eadb44972cbbd1a7ae3a520f735d43359"}, - {file = "amqp-5.1.1.tar.gz", hash = "sha256:2c1b13fecc0893e946c65cbd5f36427861cffa4ea2201d8f6fca22e2a373b5e2"}, + {file = "amqp-5.2.0-py3-none-any.whl", hash = "sha256:827cb12fb0baa892aad844fd95258143bce4027fdac4fccddbc43330fd281637"}, + {file = "amqp-5.2.0.tar.gz", hash = "sha256:a1ecff425ad063ad42a486c902807d1482311481c8ad95a72694b2975e75f7fd"}, ] [package.dependencies] -vine = ">=5.0.0" +vine = ">=5.0.0,<6.0.0" [[package]] name = "anyio" -version = "4.0.0" +version = "4.4.0" description = "High level compatibility layer for multiple asynchronous event loop implementations" -category = "main" optional = false python-versions = ">=3.8" files = [ - {file = "anyio-4.0.0-py3-none-any.whl", hash = "sha256:cfdb2b588b9fc25ede96d8db56ed50848b0b649dca3dd1df0b11f683bb9e0b5f"}, - {file = "anyio-4.0.0.tar.gz", hash = "sha256:f7ed51751b2c2add651e5747c891b47e26d2a21be5d32d9311dfe9692f3e5d7a"}, + {file = "anyio-4.4.0-py3-none-any.whl", hash = "sha256:c1b2d8f46a8a812513012e1107cb0e68c17159a7a594208005a57dc776e1bdc7"}, + {file = "anyio-4.4.0.tar.gz", hash = "sha256:5aadc6a1bbb7cdb0bede386cac5e2940f5e2ff3aa20277e991cf028e0585ce94"}, ] [package.dependencies] exceptiongroup = {version = ">=1.0.2", markers = "python_version < \"3.11\""} idna = ">=2.8" sniffio = ">=1.1" +typing-extensions = {version = ">=4.1", markers = "python_version < \"3.11\""} [package.extras] -doc = ["Sphinx (>=7)", "packaging", "sphinx-autodoc-typehints (>=1.2.0)"] -test = ["anyio[trio]", "coverage[toml] (>=7)", "hypothesis (>=4.0)", "psutil (>=5.9)", "pytest (>=7.0)", "pytest-mock (>=3.6.1)", "trustme", "uvloop (>=0.17)"] -trio = ["trio (>=0.22)"] +doc = ["Sphinx (>=7)", "packaging", "sphinx-autodoc-typehints (>=1.2.0)", "sphinx-rtd-theme"] +test = ["anyio[trio]", "coverage[toml] (>=7)", "exceptiongroup (>=1.2.0)", "hypothesis (>=4.0)", "psutil (>=5.9)", "pytest (>=7.0)", "pytest-mock (>=3.6.1)", "trustme", "uvloop (>=0.17)"] +trio = ["trio (>=0.23)"] [[package]] name = "apispec" -version = "6.3.0" +version = "6.6.1" description = "A pluggable API specification generator. Currently supports the OpenAPI Specification (f.k.a. the Swagger specification)." -category = "main" optional = false -python-versions = ">=3.7" +python-versions = ">=3.8" files = [ - {file = "apispec-6.3.0-py3-none-any.whl", hash = "sha256:95a0b9355785df998bb0e9b939237a30ee4c7428fd6ef97305eae3da06b9b339"}, - {file = "apispec-6.3.0.tar.gz", hash = "sha256:6cb08d92ce73ff0b3bf46cb2ea5c00d57289b0f279fb0256a3df468182ba5344"}, + {file = "apispec-6.6.1-py3-none-any.whl", hash = "sha256:6460315cb38ac6a2ff42d9e2b8dc0435c37d4428d3abeda96ff97b5dc8eb6b94"}, + {file = "apispec-6.6.1.tar.gz", hash = "sha256:f5caa47cee75fe03b9c50b5594048b4c052eeca2c212e0dac12dbb6175d9a659"}, ] [package.dependencies] packaging = ">=21.3" [package.extras] -dev = ["PyYAML (>=3.10)", "flake8 (==5.0.4)", "flake8-bugbear (==22.9.23)", "marshmallow (>=3.13.0)", "mypy (==0.982)", "openapi-spec-validator (<0.5)", "prance[osv] (>=0.11)", "pre-commit (>=2.4,<3.0)", "pytest", "tox", "types-PyYAML"] -docs = ["marshmallow (>=3.13.0)", "pyyaml (==6.0)", "sphinx (==5.2.3)", "sphinx-issues (==3.0.1)", "sphinx-rtd-theme (==1.0.0)"] -lint = ["flake8 (==5.0.4)", "flake8-bugbear (==22.9.23)", "mypy (==0.982)", "pre-commit (>=2.4,<3.0)", "types-PyYAML"] +dev = ["apispec[tests]", "pre-commit (>=3.5,<4.0)", "tox"] +docs = ["apispec[marshmallow]", "pyyaml (==6.0.1)", "sphinx (==7.3.7)", "sphinx-issues (==4.1.0)", "sphinx-rtd-theme (==2.0.0)"] marshmallow = ["marshmallow (>=3.18.0)"] -tests = ["PyYAML (>=3.10)", "marshmallow (>=3.13.0)", "openapi-spec-validator (<0.5)", "prance[osv] (>=0.11)", "pytest"] -validation = ["openapi-spec-validator (<0.5)", "prance[osv] (>=0.11)"] +tests = ["apispec[marshmallow,yaml]", "openapi-spec-validator (==0.7.1)", "pytest"] yaml = ["PyYAML (>=3.10)"] [[package]] name = "appnope" -version = "0.1.3" +version = "0.1.4" description = "Disable App Nap on macOS >= 10.9" -category = "main" optional = false -python-versions = "*" +python-versions = ">=3.6" files = [ - 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