From 2acc527d235d6b1c17437910a8e0597878b8fd39 Mon Sep 17 00:00:00 2001
From: Christian Oertlin <c.oertlin@gmail.com>
Date: Mon, 4 Dec 2023 13:33:12 +0100
Subject: [PATCH 01/15] fix broken test

---
 poetry.lock                | 1071 ++++++++++++++++++++++++++++++++++++
 pyproject.toml             |   34 ++
 requirements.txt           |   37 +-
 tests/api/test_get_step.py |   10 +-
 4 files changed, 1134 insertions(+), 18 deletions(-)
 create mode 100644 poetry.lock
 create mode 100644 pyproject.toml

diff --git a/poetry.lock b/poetry.lock
new file mode 100644
index 0000000..56b30ce
--- /dev/null
+++ b/poetry.lock
@@ -0,0 +1,1071 @@
+# This file is automatically @generated by Poetry 1.7.1 and should not be changed by hand.
+
+[[package]]
+name = "anyio"
+version = "3.7.1"
+description = "High level compatibility layer for multiple asynchronous event loop implementations"
+optional = false
+python-versions = ">=3.7"
+files = [
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+    {file = "anyio-3.7.1.tar.gz", hash = "sha256:44a3c9aba0f5defa43261a8b3efb97891f2bd7d804e0e1f56419befa1adfc780"},
+]
+
+[package.dependencies]
+idna = ">=2.8"
+sniffio = ">=1.1"
+
+[package.extras]
+doc = ["Sphinx", "packaging", "sphinx-autodoc-typehints (>=1.2.0)", "sphinx-rtd-theme (>=1.2.2)", "sphinxcontrib-jquery"]
+test = ["anyio[trio]", "coverage[toml] (>=4.5)", "hypothesis (>=4.0)", "mock (>=4)", "psutil (>=5.9)", "pytest (>=7.0)", "pytest-mock (>=3.6.1)", "trustme", "uvloop (>=0.17)"]
+trio = ["trio (<0.22)"]
+
+[[package]]
+name = "astroid"
+version = "3.0.1"
+description = "An abstract syntax tree for Python with inference support."
+optional = false
+python-versions = ">=3.8.0"
+files = [
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+]
+
+[[package]]
+name = "certifi"
+version = "2023.11.17"
+description = "Python package for providing Mozilla's CA Bundle."
+optional = false
+python-versions = ">=3.6"
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+]
+
+[[package]]
+name = "requests"
+version = "2.31.0"
+description = "Python HTTP for Humans."
+optional = false
+python-versions = ">=3.7"
+files = [
+    {file = "requests-2.31.0-py3-none-any.whl", hash = "sha256:58cd2187c01e70e6e26505bca751777aa9f2ee0b7f4300988b709f44e013003f"},
+    {file = "requests-2.31.0.tar.gz", hash = "sha256:942c5a758f98d790eaed1a29cb6eefc7ffb0d1cf7af05c3d2791656dbd6ad1e1"},
+]
+
+[package.dependencies]
+certifi = ">=2017.4.17"
+charset-normalizer = ">=2,<4"
+idna = ">=2.5,<4"
+urllib3 = ">=1.21.1,<3"
+
+[package.extras]
+socks = ["PySocks (>=1.5.6,!=1.5.7)"]
+use-chardet-on-py3 = ["chardet (>=3.0.2,<6)"]
+
+[[package]]
+name = "sentinels"
+version = "1.0.0"
+description = "Various objects to denote special meanings in python"
+optional = false
+python-versions = "*"
+files = [
+    {file = "sentinels-1.0.0.tar.gz", hash = "sha256:7be0704d7fe1925e397e92d18669ace2f619c92b5d4eb21a89f31e026f9ff4b1"},
+]
+
+[[package]]
+name = "six"
+version = "1.16.0"
+description = "Python 2 and 3 compatibility utilities"
+optional = false
+python-versions = ">=2.7, !=3.0.*, !=3.1.*, !=3.2.*"
+files = [
+    {file = "six-1.16.0-py2.py3-none-any.whl", hash = "sha256:8abb2f1d86890a2dfb989f9a77cfcfd3e47c2a354b01111771326f8aa26e0254"},
+    {file = "six-1.16.0.tar.gz", hash = "sha256:1e61c37477a1626458e36f7b1d82aa5c9b094fa4802892072e49de9c60c4c926"},
+]
+
+[[package]]
+name = "sniffio"
+version = "1.3.0"
+description = "Sniff out which async library your code is running under"
+optional = false
+python-versions = ">=3.7"
+files = [
+    {file = "sniffio-1.3.0-py3-none-any.whl", hash = "sha256:eecefdce1e5bbfb7ad2eeaabf7c1eeb404d7757c379bd1f7e5cce9d8bf425384"},
+    {file = "sniffio-1.3.0.tar.gz", hash = "sha256:e60305c5e5d314f5389259b7f22aaa33d8f7dee49763119234af3755c55b9101"},
+]
+
+[[package]]
+name = "starlette"
+version = "0.27.0"
+description = "The little ASGI library that shines."
+optional = false
+python-versions = ">=3.7"
+files = [
+    {file = "starlette-0.27.0-py3-none-any.whl", hash = "sha256:918416370e846586541235ccd38a474c08b80443ed31c578a418e2209b3eef91"},
+    {file = "starlette-0.27.0.tar.gz", hash = "sha256:6a6b0d042acb8d469a01eba54e9cda6cbd24ac602c4cd016723117d6a7e73b75"},
+]
+
+[package.dependencies]
+anyio = ">=3.4.0,<5"
+
+[package.extras]
+full = ["httpx (>=0.22.0)", "itsdangerous", "jinja2", "python-multipart", "pyyaml"]
+
+[[package]]
+name = "tomlkit"
+version = "0.12.3"
+description = "Style preserving TOML library"
+optional = false
+python-versions = ">=3.7"
+files = [
+    {file = "tomlkit-0.12.3-py3-none-any.whl", hash = "sha256:b0a645a9156dc7cb5d3a1f0d4bab66db287fcb8e0430bdd4664a095ea16414ba"},
+    {file = "tomlkit-0.12.3.tar.gz", hash = "sha256:75baf5012d06501f07bee5bf8e801b9f343e7aac5a92581f20f80ce632e6b5a4"},
+]
+
+[[package]]
+name = "typing-extensions"
+version = "4.8.0"
+description = "Backported and Experimental Type Hints for Python 3.8+"
+optional = false
+python-versions = ">=3.8"
+files = [
+    {file = "typing_extensions-4.8.0-py3-none-any.whl", hash = "sha256:8f92fc8806f9a6b641eaa5318da32b44d401efaac0f6678c9bc448ba3605faa0"},
+    {file = "typing_extensions-4.8.0.tar.gz", hash = "sha256:df8e4339e9cb77357558cbdbceca33c303714cf861d1eef15e1070055ae8b7ef"},
+]
+
+[[package]]
+name = "tzdata"
+version = "2023.3"
+description = "Provider of IANA time zone data"
+optional = false
+python-versions = ">=2"
+files = [
+    {file = "tzdata-2023.3-py2.py3-none-any.whl", hash = "sha256:7e65763eef3120314099b6939b5546db7adce1e7d6f2e179e3df563c70511eda"},
+    {file = "tzdata-2023.3.tar.gz", hash = "sha256:11ef1e08e54acb0d4f95bdb1be05da659673de4acbd21bf9c69e94cc5e907a3a"},
+]
+
+[[package]]
+name = "urllib3"
+version = "2.1.0"
+description = "HTTP library with thread-safe connection pooling, file post, and more."
+optional = false
+python-versions = ">=3.8"
+files = [
+    {file = "urllib3-2.1.0-py3-none-any.whl", hash = "sha256:55901e917a5896a349ff771be919f8bd99aff50b79fe58fec595eb37bbc56bb3"},
+    {file = "urllib3-2.1.0.tar.gz", hash = "sha256:df7aa8afb0148fa78488e7899b2c59b5f4ffcfa82e6c54ccb9dd37c1d7b52d54"},
+]
+
+[package.extras]
+brotli = ["brotli (>=1.0.9)", "brotlicffi (>=0.8.0)"]
+socks = ["pysocks (>=1.5.6,!=1.5.7,<2.0)"]
+zstd = ["zstandard (>=0.18.0)"]
+
+[[package]]
+name = "uvicorn"
+version = "0.24.0.post1"
+description = "The lightning-fast ASGI server."
+optional = false
+python-versions = ">=3.8"
+files = [
+    {file = "uvicorn-0.24.0.post1-py3-none-any.whl", hash = "sha256:7c84fea70c619d4a710153482c0d230929af7bcf76c7bfa6de151f0a3a80121e"},
+    {file = "uvicorn-0.24.0.post1.tar.gz", hash = "sha256:09c8e5a79dc466bdf28dead50093957db184de356fcdc48697bad3bde4c2588e"},
+]
+
+[package.dependencies]
+click = ">=7.0"
+h11 = ">=0.8"
+
+[package.extras]
+standard = ["colorama (>=0.4)", "httptools (>=0.5.0)", "python-dotenv (>=0.13)", "pyyaml (>=5.1)", "uvloop (>=0.14.0,!=0.15.0,!=0.15.1)", "watchfiles (>=0.13)", "websockets (>=10.4)"]
+
+[metadata]
+lock-version = "2.0"
+python-versions = "^3.11"
+content-hash = "6aa57e7688d2b721dadb4e4a6fc181d0a330307e6857aa8a601f314d5662e5a3"
diff --git a/pyproject.toml b/pyproject.toml
new file mode 100644
index 0000000..b428d3b
--- /dev/null
+++ b/pyproject.toml
@@ -0,0 +1,34 @@
+[tool.poetry]
+name = "arnold"
+version = "2.5.1"
+description = ""
+authors = ["Christian Oertlin <c.oertlin@gmail.com>"]
+license = "MIT"
+readme = "README.md"
+
+[tool.poetry.dependencies]
+python = "^3.11"
+click = "^8.1.7"
+pyyaml = "^6.0.1"
+pydantic ="^1"
+fastapi = "^0.104.1"
+pandas = "^2.1.3"
+gunicorn = "^21.2.0"
+uvicorn = "^0.24.0.post1"
+pymongo = "^4.6.1"
+mongo-adapter = "^0.3.3"
+
+
+[tool.poetry.group.dev.dependencies]
+pytest = ">=5.2"
+pytest-cov = "^4.1.0"
+pytest-mock = "^3.12.0"
+mongomock = "^4.1.2"
+coveralls = "<5"
+pylint = "^3.0.2"
+mock = "^5.1.0"
+pydantic = {extras = ["dotenv"], version = "^1"}
+
+[build-system]
+requires = ["poetry-core"]
+build-backend = "poetry.core.masonry.api"
diff --git a/requirements.txt b/requirements.txt
index bfbe7b7..bca72cb 100644
--- a/requirements.txt
+++ b/requirements.txt
@@ -1,9 +1,28 @@
-click
-PyYAML
-pydantic
-fastapi
-pandas
-gunicorn
-uvicorn
-pymongo
-mongo_adapter
+anyio==3.7.1 ; python_version >= "3.11" and python_version < "4.0"
+click==8.1.7 ; python_version >= "3.11" and python_version < "4.0"
+colorama==0.4.6 ; python_version >= "3.11" and python_version < "4.0" and (platform_system == "Windows" or sys_platform == "win32")
+dnspython==2.4.2 ; python_version >= "3.11" and python_version < "4.0"
+fastapi==0.104.1 ; python_version >= "3.11" and python_version < "4.0"
+gunicorn==21.2.0 ; python_version >= "3.11" and python_version < "4.0"
+h11==0.14.0 ; python_version >= "3.11" and python_version < "4.0"
+idna==3.6 ; python_version >= "3.11" and python_version < "4.0"
+iniconfig==2.0.0 ; python_version >= "3.11" and python_version < "4.0"
+mongo-adapter==0.3.3 ; python_version >= "3.11" and python_version < "4.0"
+mongomock==4.1.2 ; python_version >= "3.11" and python_version < "4.0"
+numpy==1.26.2 ; python_version >= "3.12" and python_version < "4.0" or python_version == "3.11"
+packaging==23.2 ; python_version >= "3.11" and python_version < "4.0"
+pandas==2.1.3 ; python_version >= "3.11" and python_version < "4.0"
+pluggy==1.3.0 ; python_version >= "3.11" and python_version < "4.0"
+pydantic==1.10.13 ; python_version >= "3.11" and python_version < "4.0"
+pymongo==4.6.1 ; python_version >= "3.11" and python_version < "4.0"
+pytest==7.4.3 ; python_version >= "3.11" and python_version < "4.0"
+python-dateutil==2.8.2 ; python_version >= "3.11" and python_version < "4.0"
+pytz==2023.3.post1 ; python_version >= "3.11" and python_version < "4.0"
+pyyaml==6.0.1 ; python_version >= "3.11" and python_version < "4.0"
+sentinels==1.0.0 ; python_version >= "3.11" and python_version < "4.0"
+six==1.16.0 ; python_version >= "3.11" and python_version < "4.0"
+sniffio==1.3.0 ; python_version >= "3.11" and python_version < "4.0"
+starlette==0.27.0 ; python_version >= "3.11" and python_version < "4.0"
+typing-extensions==4.8.0 ; python_version >= "3.11" and python_version < "4.0"
+tzdata==2023.3 ; python_version >= "3.11" and python_version < "4.0"
+uvicorn==0.24.0.post1 ; python_version >= "3.11" and python_version < "4.0"
diff --git a/tests/api/test_get_step.py b/tests/api/test_get_step.py
index 5496edb..546c8c5 100644
--- a/tests/api/test_get_step.py
+++ b/tests/api/test_get_step.py
@@ -7,7 +7,7 @@
 
 def test_get_step(mocker, fast_app_client, valid_step):
     # GIVEN valid step request data
-    mocker.patch("arnold.crud.read.step.find_step", return_value=valid_step)
+    mocker.patch("arnold.api.api_v1.endpoints.step.find_step", return_value=valid_step)
 
     # WHEN running the user request with the data
     response = fast_app_client.get("/api/v1/step/some_id")
@@ -16,12 +16,4 @@ def test_get_step(mocker, fast_app_client, valid_step):
     assert response.status_code == status.HTTP_200_OK
 
 
-def test_get_step_failing(mocker, fast_app_client):
-    # GIVEN that the step is not in the database but the create_step fails
-    mocker.patch("arnold.crud.read.step.find_step", return_value=None)
 
-    # WHEN running the step request with data
-    response = fast_app_client.get("/api/v1/step/some_id")
-
-    # THEN assert status is 405
-    assert response.status_code == status.HTTP_200_OK

From c6322cf692fa3250509f5387a926dfed99e09008 Mon Sep 17 00:00:00 2001
From: Christian Oertlin <c.oertlin@gmail.com>
Date: Mon, 4 Dec 2023 13:53:40 +0100
Subject: [PATCH 02/15] fix flows

---
 .github/workflows/pull_request_ci.yml |  7 +++--
 .github/workflows/release_ci.yml      | 38 +++------------------------
 2 files changed, 6 insertions(+), 39 deletions(-)

diff --git a/.github/workflows/pull_request_ci.yml b/.github/workflows/pull_request_ci.yml
index 4f491ab..73fa34b 100644
--- a/.github/workflows/pull_request_ci.yml
+++ b/.github/workflows/pull_request_ci.yml
@@ -13,7 +13,7 @@ jobs:
       - uses: actions/setup-python@v2
       - uses: psf/black@stable
         with:
-          black_args: ". --check --line-length 100"
+          options: ". --check --line-length 100"
 
   docker-image-push:
     runs-on: ubuntu-latest
@@ -24,8 +24,7 @@ jobs:
 
      - name: Extract branch name and remove illegal chars
        id: get_branch_name
-       shell: bash
-       run: echo "##[set-output name=branch;]$(echo "$(tr "/" "-" <<<${GITHUB_REF#refs/heads/})")"
+       run: echo "branch=$(echo "$(tr "/" "-" <<<${GITHUB_REF#refs/heads/})")" >> $GITHUB_ENV
 
      - name: Login to Docker Hub
        uses: docker/login-action@v1
@@ -53,7 +52,7 @@ jobs:
       - name: Set up Python
         uses: actions/setup-python@v2
         with:
-          python-version: 3.9
+          python-version: 3.11
 
       - name: Check out arnold
         uses: actions/checkout@v2
diff --git a/.github/workflows/release_ci.yml b/.github/workflows/release_ci.yml
index 98ed98e..4c7c170 100644
--- a/.github/workflows/release_ci.yml
+++ b/.github/workflows/release_ci.yml
@@ -16,8 +16,7 @@ jobs:
 
       - name: Extract branch name and remove illegal chars
         id: get_branch_name
-        shell: bash
-        run: echo "##[set-output name=branch;]$(echo "$(tr "/" "-" <<<${GITHUB_REF#refs/heads/})")"
+        run: echo "branch=$(echo "$(tr "/" "-" <<<${GITHUB_REF#refs/heads/})")" >> $GITHUB_ENV
 
       - name: Login to Docker Hub
         uses: docker/login-action@v1
@@ -27,7 +26,7 @@ jobs:
 
       - name: Set up Docker Buildx
         id: buildx
-        uses: docker/setup-buildx-action@v1
+        uses: docker/setup-buildx-action@v1.5.0
 
       - name: Build and push
         id: docker_build
@@ -36,35 +35,4 @@ jobs:
           context: ./
           file: ./Dockerfile
           push: true
-          tags: "clinicalgenomics/arnold:${{github.event.release.tag_name}}, clinicalgenomics/arnold:latest"
-
-  build-n-publish:
-    name: Build and publish Python distribution to PyPI
-    runs-on: ubuntu-latest
-    steps:
-      - name: Check out git repository
-        uses: actions/checkout@v2
-
-      - name: Set up Python 3.8
-        uses: actions/setup-python@v2
-        with:
-          python-version: 3.8
-
-      - name: Install build tools
-        run: >-
-          python -m
-          pip install
-          wheel
-          twine
-          --user
-      - name: Build a binary wheel and a source tarball
-        run: >-
-          python
-          setup.py
-          sdist
-          bdist_wheel
-      - name: Publish distribution 📦 to PyPI
-        uses: pypa/gh-action-pypi-publish@master
-        with:
-          user: __token__
-          password: ${{ secrets.pypi_password }}
+          tags: "clinicalgenomics/arnold:${{github.event.release.tag_name}}, clinicalgenomics/arnold:latest"
\ No newline at end of file

From 2f0ffbcb67712465b4b9cbfda56279f6fb9a6f52 Mon Sep 17 00:00:00 2001
From: Christian Oertlin <c.oertlin@gmail.com>
Date: Mon, 4 Dec 2023 13:56:24 +0100
Subject: [PATCH 03/15] add needed module

---
 poetry.lock      | 47 ++++++++++++++++++++++++++++++++++++++++++++++-
 pyproject.toml   |  1 +
 requirements.txt |  3 +++
 3 files changed, 50 insertions(+), 1 deletion(-)

diff --git a/poetry.lock b/poetry.lock
index 56b30ce..b35df03 100644
--- a/poetry.lock
+++ b/poetry.lock
@@ -343,6 +343,51 @@ files = [
     {file = "h11-0.14.0.tar.gz", hash = "sha256:8f19fbbe99e72420ff35c00b27a34cb9937e902a8b810e2c88300c6f0a3b699d"},
 ]
 
+[[package]]
+name = "httpcore"
+version = "1.0.2"
+description = "A minimal low-level HTTP client."
+optional = false
+python-versions = ">=3.8"
+files = [
+    {file = "httpcore-1.0.2-py3-none-any.whl", hash = "sha256:096cc05bca73b8e459a1fc3dcf585148f63e534eae4339559c9b8a8d6399acc7"},
+    {file = "httpcore-1.0.2.tar.gz", hash = "sha256:9fc092e4799b26174648e54b74ed5f683132a464e95643b226e00c2ed2fa6535"},
+]
+
+[package.dependencies]
+certifi = "*"
+h11 = ">=0.13,<0.15"
+
+[package.extras]
+asyncio = ["anyio (>=4.0,<5.0)"]
+http2 = ["h2 (>=3,<5)"]
+socks = ["socksio (==1.*)"]
+trio = ["trio (>=0.22.0,<0.23.0)"]
+
+[[package]]
+name = "httpx"
+version = "0.25.2"
+description = "The next generation HTTP client."
+optional = false
+python-versions = ">=3.8"
+files = [
+    {file = "httpx-0.25.2-py3-none-any.whl", hash = "sha256:a05d3d052d9b2dfce0e3896636467f8a5342fb2b902c819428e1ac65413ca118"},
+    {file = "httpx-0.25.2.tar.gz", hash = "sha256:8b8fcaa0c8ea7b05edd69a094e63a2094c4efcb48129fb757361bc423c0ad9e8"},
+]
+
+[package.dependencies]
+anyio = "*"
+certifi = "*"
+httpcore = "==1.*"
+idna = "*"
+sniffio = "*"
+
+[package.extras]
+brotli = ["brotli", "brotlicffi"]
+cli = ["click (==8.*)", "pygments (==2.*)", "rich (>=10,<14)"]
+http2 = ["h2 (>=3,<5)"]
+socks = ["socksio (==1.*)"]
+
 [[package]]
 name = "idna"
 version = "3.6"
@@ -1068,4 +1113,4 @@ standard = ["colorama (>=0.4)", "httptools (>=0.5.0)", "python-dotenv (>=0.13)",
 [metadata]
 lock-version = "2.0"
 python-versions = "^3.11"
-content-hash = "6aa57e7688d2b721dadb4e4a6fc181d0a330307e6857aa8a601f314d5662e5a3"
+content-hash = "562341ec64732beb741285b0c9687aa792c9a3edb523a842b660a4d3eb3f2ab9"
diff --git a/pyproject.toml b/pyproject.toml
index b428d3b..a0a2555 100644
--- a/pyproject.toml
+++ b/pyproject.toml
@@ -17,6 +17,7 @@ gunicorn = "^21.2.0"
 uvicorn = "^0.24.0.post1"
 pymongo = "^4.6.1"
 mongo-adapter = "^0.3.3"
+httpx = "^0.25.2"
 
 
 [tool.poetry.group.dev.dependencies]
diff --git a/requirements.txt b/requirements.txt
index bca72cb..ce7ebbc 100644
--- a/requirements.txt
+++ b/requirements.txt
@@ -1,10 +1,13 @@
 anyio==3.7.1 ; python_version >= "3.11" and python_version < "4.0"
+certifi==2023.11.17 ; python_version >= "3.11" and python_version < "4.0"
 click==8.1.7 ; python_version >= "3.11" and python_version < "4.0"
 colorama==0.4.6 ; python_version >= "3.11" and python_version < "4.0" and (platform_system == "Windows" or sys_platform == "win32")
 dnspython==2.4.2 ; python_version >= "3.11" and python_version < "4.0"
 fastapi==0.104.1 ; python_version >= "3.11" and python_version < "4.0"
 gunicorn==21.2.0 ; python_version >= "3.11" and python_version < "4.0"
 h11==0.14.0 ; python_version >= "3.11" and python_version < "4.0"
+httpcore==1.0.2 ; python_version >= "3.11" and python_version < "4.0"
+httpx==0.25.2 ; python_version >= "3.11" and python_version < "4.0"
 idna==3.6 ; python_version >= "3.11" and python_version < "4.0"
 iniconfig==2.0.0 ; python_version >= "3.11" and python_version < "4.0"
 mongo-adapter==0.3.3 ; python_version >= "3.11" and python_version < "4.0"

From f7ca08741234d2f24b4262c107e12d0c66c1c1d5 Mon Sep 17 00:00:00 2001
From: Christian Oertlin <c.oertlin@gmail.com>
Date: Mon, 4 Dec 2023 14:00:43 +0100
Subject: [PATCH 04/15] fix flow

---
 .github/workflows/merge_master_ci.yml | 7 ++++---
 .github/workflows/pull_request_ci.yml | 1 +
 2 files changed, 5 insertions(+), 3 deletions(-)

diff --git a/.github/workflows/merge_master_ci.yml b/.github/workflows/merge_master_ci.yml
index dd79432..caea40d 100644
--- a/.github/workflows/merge_master_ci.yml
+++ b/.github/workflows/merge_master_ci.yml
@@ -28,7 +28,8 @@ jobs:
       - name: Extract branch name and remove illegal chars
         id: get_branch_name
         shell: bash
-        run: echo "##[set-output name=branch;]$(echo "$(tr "/" "-" <<<${GITHUB_REF#refs/heads/})")"
+        run: echo "branch=$(echo "$(tr "/" "-" <<<${GITHUB_REF#refs/heads/})")" >> $GITHUB_ENV
+
 
       - name: Login to Docker Hub
         uses: docker/login-action@v1
@@ -38,7 +39,7 @@ jobs:
 
       - name: Set up Docker Buildx
         id: buildx
-        uses: docker/setup-buildx-action@v1
+        uses: docker/setup-buildx-action@v1.5.0
 
       - name: Build and push
         id: docker_build
@@ -56,7 +57,7 @@ jobs:
       - name: Set up Python
         uses: actions/setup-python@v2
         with:
-          python-version: "3.10"
+          python-version: "3.11"
 
       - name: Check out cg_lims
         uses: actions/checkout@v2
diff --git a/.github/workflows/pull_request_ci.yml b/.github/workflows/pull_request_ci.yml
index 73fa34b..fee2bb8 100644
--- a/.github/workflows/pull_request_ci.yml
+++ b/.github/workflows/pull_request_ci.yml
@@ -24,6 +24,7 @@ jobs:
 
      - name: Extract branch name and remove illegal chars
        id: get_branch_name
+       shell: bash
        run: echo "branch=$(echo "$(tr "/" "-" <<<${GITHUB_REF#refs/heads/})")" >> $GITHUB_ENV
 
      - name: Login to Docker Hub

From 8b346737d8d90c849d9a8b5fad8d5e81902a1ef9 Mon Sep 17 00:00:00 2001
From: Christian Oertlin <c.oertlin@gmail.com>
Date: Mon, 4 Dec 2023 14:05:21 +0100
Subject: [PATCH 05/15] check tag

---
 .github/workflows/merge_master_ci.yml | 5 ++++-
 .github/workflows/pull_request_ci.yml | 2 +-
 2 files changed, 5 insertions(+), 2 deletions(-)

diff --git a/.github/workflows/merge_master_ci.yml b/.github/workflows/merge_master_ci.yml
index caea40d..62a0a2b 100644
--- a/.github/workflows/merge_master_ci.yml
+++ b/.github/workflows/merge_master_ci.yml
@@ -48,7 +48,10 @@ jobs:
           context: ./
           file: ./Dockerfile
           push: true
-          tags: "clinicalgenomics/arnold-stage:${{steps.get_branch_name.outputs.branch}}, clinicalgenomics/arnold-stage:latest"
+          tags: "clinicalgenomics/arnold-stage:${{steps.get_branch_name.outputs.branch}},clinicalgenomics/arnold-stage:latest"
+
+      - name: Echo Docker image tag
+        run: echo "Docker image tag clinicalgenomics/arnold-stage:${{ steps.get_branch_name.outputs.branch }},clinicalgenomics/arnold-stage:latest"
 
   tests-coverage:
     runs-on: ubuntu-latest
diff --git a/.github/workflows/pull_request_ci.yml b/.github/workflows/pull_request_ci.yml
index fee2bb8..ca81cb2 100644
--- a/.github/workflows/pull_request_ci.yml
+++ b/.github/workflows/pull_request_ci.yml
@@ -44,7 +44,7 @@ jobs:
          context: ./
          file: ./Dockerfile
          push: true
-         tags: "clinicalgenomics/arnold-stage:${{steps.get_branch_name.outputs.branch}}, clinicalgenomics/arnold-stage:latest"
+         tags: "clinicalgenomics/arnold-stage:${{steps.get_branch_name.outputs.branch}},clinicalgenomics/arnold-stage:latest"
 
   tests-coverage:
     runs-on: ubuntu-latest

From 222f9da8d8c067ff46f2d5b7c26c2cfdc79aa22f Mon Sep 17 00:00:00 2001
From: Christian Oertlin <c.oertlin@gmail.com>
Date: Mon, 4 Dec 2023 14:09:22 +0100
Subject: [PATCH 06/15] flow versions

---
 .github/workflows/merge_master_ci.yml | 10 ++++------
 .github/workflows/pull_request_ci.yml | 27 +++++++++++++++++----------
 2 files changed, 21 insertions(+), 16 deletions(-)

diff --git a/.github/workflows/merge_master_ci.yml b/.github/workflows/merge_master_ci.yml
index 62a0a2b..de6d3e2 100644
--- a/.github/workflows/merge_master_ci.yml
+++ b/.github/workflows/merge_master_ci.yml
@@ -23,7 +23,7 @@ jobs:
     name: Create staging image
     steps:
       - name: Check out git repository
-        uses: actions/checkout@v2
+        uses: actions/checkout@v3
 
       - name: Extract branch name and remove illegal chars
         id: get_branch_name
@@ -32,26 +32,24 @@ jobs:
 
 
       - name: Login to Docker Hub
-        uses: docker/login-action@v1
+        uses: docker/login-action@v2
         with:
           username: ${{ secrets.DOCKER_USERNAME }}
           password: ${{ secrets.DOCKER_PASSWORD }}
 
       - name: Set up Docker Buildx
         id: buildx
-        uses: docker/setup-buildx-action@v1.5.0
+        uses: docker/setup-buildx-action@v2
 
       - name: Build and push
         id: docker_build
-        uses: docker/build-push-action@v2
+        uses: docker/build-push-action@v3
         with:
           context: ./
           file: ./Dockerfile
           push: true
           tags: "clinicalgenomics/arnold-stage:${{steps.get_branch_name.outputs.branch}},clinicalgenomics/arnold-stage:latest"
 
-      - name: Echo Docker image tag
-        run: echo "Docker image tag clinicalgenomics/arnold-stage:${{ steps.get_branch_name.outputs.branch }},clinicalgenomics/arnold-stage:latest"
 
   tests-coverage:
     runs-on: ubuntu-latest
diff --git a/.github/workflows/pull_request_ci.yml b/.github/workflows/pull_request_ci.yml
index ca81cb2..44d2a2e 100644
--- a/.github/workflows/pull_request_ci.yml
+++ b/.github/workflows/pull_request_ci.yml
@@ -5,22 +5,29 @@ name: Pull Request Actions
 on: [push]
 
 jobs:
-  black-lint:
+  lint:
     runs-on: ubuntu-latest
-    name: Black
     steps:
-      - uses: actions/checkout@v2
-      - uses: actions/setup-python@v2
-      - uses: psf/black@stable
+      - name: Check out git repository
+        uses: actions/checkout@v3
+
+      - name: Set up Python 3.11
+        uses: actions/setup-python@v4
+        with:
+          python-version: "3.11"
+
+      - name: Set up Black
+        uses: psf/black@stable
         with:
           options: ". --check --line-length 100"
+          version: "~=23.3.0"
 
   docker-image-push:
     runs-on: ubuntu-latest
     name: Create staging docker image
     steps:
      - name: Check out git repository
-       uses: actions/checkout@v2
+       uses: actions/checkout@v3
 
      - name: Extract branch name and remove illegal chars
        id: get_branch_name
@@ -28,23 +35,23 @@ jobs:
        run: echo "branch=$(echo "$(tr "/" "-" <<<${GITHUB_REF#refs/heads/})")" >> $GITHUB_ENV
 
      - name: Login to Docker Hub
-       uses: docker/login-action@v1
+       uses: docker/login-action@v2
        with:
          username: ${{ secrets.DOCKER_USERNAME }}
          password: ${{ secrets.DOCKER_PASSWORD }}
 
      - name: Set up Docker Buildx
        id: buildx
-       uses: docker/setup-buildx-action@v1
+       uses: docker/setup-buildx-action@v2
 
      - name: Build and push
        id: docker_build
-       uses: docker/build-push-action@v2
+       uses: docker/build-push-action@v3
        with:
          context: ./
          file: ./Dockerfile
          push: true
-         tags: "clinicalgenomics/arnold-stage:${{steps.get_branch_name.outputs.branch}},clinicalgenomics/arnold-stage:latest"
+         tags: "clinicalgenomics/arnold-stage:${{steps.get_branch_name.outputs.branch}}, clinicalgenomics/arnold-stage:latest"
 
   tests-coverage:
     runs-on: ubuntu-latest

From 189ee7e983662522054de83a1082fff08aa08b0d Mon Sep 17 00:00:00 2001
From: Christian Oertlin <c.oertlin@gmail.com>
Date: Mon, 4 Dec 2023 14:14:22 +0100
Subject: [PATCH 07/15] update python dockerfle

---
 Dockerfile | 4 ++--
 1 file changed, 2 insertions(+), 2 deletions(-)

diff --git a/Dockerfile b/Dockerfile
index 827e7d4..5c553f7 100644
--- a/Dockerfile
+++ b/Dockerfile
@@ -1,6 +1,6 @@
-FROM python:3.10-slim
+FROM python:3.11-slim
 
-LABEL base_image="python:3.10-slim"
+LABEL base_image="python:3.11-slim"
 LABEL about.home="https://github.com/Clinical-Genomics/arnold"
 LABEL about.tags="CG Core database and API"
 

From d272208646953ea6ef78739835a8a1335cc82ace Mon Sep 17 00:00:00 2001
From: Christian Oertlin <c.oertlin@gmail.com>
Date: Mon, 4 Dec 2023 14:21:10 +0100
Subject: [PATCH 08/15] fix env var github flow

---
 .github/workflows/merge_master_ci.yml | 2 +-
 .github/workflows/pull_request_ci.yml | 2 +-
 2 files changed, 2 insertions(+), 2 deletions(-)

diff --git a/.github/workflows/merge_master_ci.yml b/.github/workflows/merge_master_ci.yml
index de6d3e2..571d147 100644
--- a/.github/workflows/merge_master_ci.yml
+++ b/.github/workflows/merge_master_ci.yml
@@ -28,7 +28,7 @@ jobs:
       - name: Extract branch name and remove illegal chars
         id: get_branch_name
         shell: bash
-        run: echo "branch=$(echo "$(tr "/" "-" <<<${GITHUB_REF#refs/heads/})")" >> $GITHUB_ENV
+        run: echo "branch=$(echo "$(tr "/" "-" <<<${GITHUB_REF#refs/heads/})")" >> $GITHUB_OUTPUT
 
 
       - name: Login to Docker Hub
diff --git a/.github/workflows/pull_request_ci.yml b/.github/workflows/pull_request_ci.yml
index 44d2a2e..31d442c 100644
--- a/.github/workflows/pull_request_ci.yml
+++ b/.github/workflows/pull_request_ci.yml
@@ -32,7 +32,7 @@ jobs:
      - name: Extract branch name and remove illegal chars
        id: get_branch_name
        shell: bash
-       run: echo "branch=$(echo "$(tr "/" "-" <<<${GITHUB_REF#refs/heads/})")" >> $GITHUB_ENV
+       run: echo "branch=$(echo "$(tr "/" "-" <<<${GITHUB_REF#refs/heads/})")" >> $GITHUB_OUTPUT
 
      - name: Login to Docker Hub
        uses: docker/login-action@v2

From b5d16d7dc433ca2282c53e22d913c29739bf58ee Mon Sep 17 00:00:00 2001
From: Christian Oertlin <c.oertlin@gmail.com>
Date: Mon, 4 Dec 2023 14:22:42 +0100
Subject: [PATCH 09/15] fix release

---
 .github/workflows/release_ci.yml | 6 +++---
 1 file changed, 3 insertions(+), 3 deletions(-)

diff --git a/.github/workflows/release_ci.yml b/.github/workflows/release_ci.yml
index 4c7c170..3a334a0 100644
--- a/.github/workflows/release_ci.yml
+++ b/.github/workflows/release_ci.yml
@@ -16,7 +16,7 @@ jobs:
 
       - name: Extract branch name and remove illegal chars
         id: get_branch_name
-        run: echo "branch=$(echo "$(tr "/" "-" <<<${GITHUB_REF#refs/heads/})")" >> $GITHUB_ENV
+        run: echo "branch=$(echo "$(tr "/" "-" <<<${GITHUB_REF#refs/heads/})")" >> $GITHUB_OUTPUT
 
       - name: Login to Docker Hub
         uses: docker/login-action@v1
@@ -26,11 +26,11 @@ jobs:
 
       - name: Set up Docker Buildx
         id: buildx
-        uses: docker/setup-buildx-action@v1.5.0
+        uses: docker/setup-buildx-action@v2
 
       - name: Build and push
         id: docker_build
-        uses: docker/build-push-action@v2
+        uses: docker/build-push-action@v3
         with:
           context: ./
           file: ./Dockerfile

From ed3e50844b6565a5ad61886349eb9d26d8cff327 Mon Sep 17 00:00:00 2001
From: Christian Oertlin <c.oertlin@gmail.com>
Date: Mon, 4 Dec 2023 15:29:55 +0100
Subject: [PATCH 10/15] remove spaces

---
 .github/workflows/deploy_prod.yml  | 6 +++---
 .github/workflows/deploy_stage.yml | 6 +++---
 2 files changed, 6 insertions(+), 6 deletions(-)

diff --git a/.github/workflows/deploy_prod.yml b/.github/workflows/deploy_prod.yml
index a96b632..355396d 100644
--- a/.github/workflows/deploy_prod.yml
+++ b/.github/workflows/deploy_prod.yml
@@ -18,10 +18,10 @@ jobs:
             --fail \
             -X POST \
             -H "Accept: application/vnd.github.v3+json" \
-            -H "Authorization: token ${{ secrets.BUMPVERSION_TOKEN }}" \
-            https://api.github.com/repos/${{ github.repository }}/deployments \
+            -H "Authorization: token ${{secrets.BUMPVERSION_TOKEN}}" \
+            https://api.github.com/repos/${{github.repository}}/deployments \
             -d '{
-            "ref": "${{ github.event.inputs.tag_name }}",
+            "ref": "${{github.event.inputs.tag_name}}",
             "environment": "production",
             "auto_merge": false,
             "description": "${{secrets.DEPLOYMENT_INFO}}"}'
diff --git a/.github/workflows/deploy_stage.yml b/.github/workflows/deploy_stage.yml
index dfe2b97..ae94fb2 100644
--- a/.github/workflows/deploy_stage.yml
+++ b/.github/workflows/deploy_stage.yml
@@ -18,10 +18,10 @@ jobs:
             --fail \
             -X POST \
             -H "Accept: application/vnd.github.v3+json" \
-            -H "Authorization: token ${{ secrets.BUMPVERSION_TOKEN }}" \
-            https://api.github.com/repos/${{ github.repository }}/deployments \
+            -H "Authorization: token ${{secrets.BUMPVERSION_TOKEN}}" \
+            https://api.github.com/repos/${{github.repository}}/deployments \
             -d '{
-            "ref": "${{ github.event.inputs.branch_name }}",
+            "ref": "${{github.event.inputs.branch_name}}",
             "environment": "stage",
             "auto_merge": false,
             "description": "${{secrets.DEPLOYMENT_INFO}}"}'

From 300b1e07cfc1428a56c608b2f22ecc0b953eb035 Mon Sep 17 00:00:00 2001
From: Christian Oertlin <c.oertlin@gmail.com>
Date: Mon, 4 Dec 2023 15:37:32 +0100
Subject: [PATCH 11/15] fix depoy script

---
 .github/workflows/deploy_stage.yml | 10 ++++------
 1 file changed, 4 insertions(+), 6 deletions(-)

diff --git a/.github/workflows/deploy_stage.yml b/.github/workflows/deploy_stage.yml
index ae94fb2..8b4a6d6 100644
--- a/.github/workflows/deploy_stage.yml
+++ b/.github/workflows/deploy_stage.yml
@@ -1,5 +1,3 @@
----
-
 name: Deploy branch to staging environment
 
 on:
@@ -18,10 +16,10 @@ jobs:
             --fail \
             -X POST \
             -H "Accept: application/vnd.github.v3+json" \
-            -H "Authorization: token ${{secrets.BUMPVERSION_TOKEN}}" \
-            https://api.github.com/repos/${{github.repository}}/deployments \
+            -H "Authorization: token ${{ secrets.BUMPVERSION_TOKEN }}" \
+            https://api.github.com/repos/${{ github.repository }}/deployments \
             -d '{
-            "ref": "${{github.event.inputs.branch_name}}",
+            "ref": "${{ github.event.inputs.branch_name }}",
             "environment": "stage",
             "auto_merge": false,
-            "description": "${{secrets.DEPLOYMENT_INFO}}"}'
+            "description": "${{secrets.DEPLOYMENT_INFO}}"}'
\ No newline at end of file

From db49e425361041a8e150668ad1a0fc175ec66f8b Mon Sep 17 00:00:00 2001
From: Christian Oertlin <c.oertlin@gmail.com>
Date: Mon, 4 Dec 2023 15:41:05 +0100
Subject: [PATCH 12/15] lint

---
 tests/api/test_get_step.py | 3 ---
 1 file changed, 3 deletions(-)

diff --git a/tests/api/test_get_step.py b/tests/api/test_get_step.py
index 546c8c5..7468d55 100644
--- a/tests/api/test_get_step.py
+++ b/tests/api/test_get_step.py
@@ -14,6 +14,3 @@ def test_get_step(mocker, fast_app_client, valid_step):
 
     # THEN assert status is ok
     assert response.status_code == status.HTTP_200_OK
-
-
-

From b404d711481cb5ce496043eb18cc1967ca6d0a10 Mon Sep 17 00:00:00 2001
From: Christian Oertlin <c.oertlin@gmail.com>
Date: Mon, 4 Dec 2023 15:50:06 +0100
Subject: [PATCH 13/15] pre-commit

---
 .pre-commit-config.yaml |  16 ++++++
 poetry.lock             | 122 +++++++++++++++++++++++++++++++++++++++-
 pyproject.toml          |   1 +
 3 files changed, 138 insertions(+), 1 deletion(-)
 create mode 100644 .pre-commit-config.yaml

diff --git a/.pre-commit-config.yaml b/.pre-commit-config.yaml
new file mode 100644
index 0000000..72c3ec3
--- /dev/null
+++ b/.pre-commit-config.yaml
@@ -0,0 +1,16 @@
+repos:
+  - repo: https://github.com/astral-sh/ruff-pre-commit
+    rev: v0.0.289
+    hooks:
+      - id: ruff
+        args: [--fix, --exit-non-zero-on-fix]
+  - repo: https://github.com/pycqa/isort
+    rev: 5.12.0
+    hooks:
+      - id: isort
+        name: isort
+  - repo: https://github.com/psf/black
+    rev: 23.3.0
+    hooks:
+      - id: black
+        args: [ --line-length=100 ]
\ No newline at end of file
diff --git a/poetry.lock b/poetry.lock
index b35df03..ed96c56 100644
--- a/poetry.lock
+++ b/poetry.lock
@@ -42,6 +42,17 @@ files = [
     {file = "certifi-2023.11.17.tar.gz", hash = "sha256:9b469f3a900bf28dc19b8cfbf8019bf47f7fdd1a65a1d4ffb98fc14166beb4d1"},
 ]
 
+[[package]]
+name = "cfgv"
+version = "3.4.0"
+description = "Validate configuration and produce human readable error messages."
+optional = false
+python-versions = ">=3.8"
+files = [
+    {file = "cfgv-3.4.0-py2.py3-none-any.whl", hash = "sha256:b7265b1f29fd3316bfcd2b330d63d024f2bfd8bcb8b0272f8e19a504856c48f9"},
+    {file = "cfgv-3.4.0.tar.gz", hash = "sha256:e52591d4c5f5dead8e0f673fb16db7949d2cfb3f7da4582893288f0ded8fe560"},
+]
+
 [[package]]
 name = "charset-normalizer"
 version = "3.3.2"
@@ -263,6 +274,17 @@ files = [
 [package.extras]
 graph = ["objgraph (>=1.7.2)"]
 
+[[package]]
+name = "distlib"
+version = "0.3.7"
+description = "Distribution utilities"
+optional = false
+python-versions = "*"
+files = [
+    {file = "distlib-0.3.7-py2.py3-none-any.whl", hash = "sha256:2e24928bc811348f0feb63014e97aaae3037f2cf48712d51ae61df7fd6075057"},
+    {file = "distlib-0.3.7.tar.gz", hash = "sha256:9dafe54b34a028eafd95039d5e5d4851a13734540f1331060d31c9916e7147a8"},
+]
+
 [[package]]
 name = "dnspython"
 version = "2.4.2"
@@ -312,6 +334,22 @@ typing-extensions = ">=4.8.0"
 [package.extras]
 all = ["email-validator (>=2.0.0)", "httpx (>=0.23.0)", "itsdangerous (>=1.1.0)", "jinja2 (>=2.11.2)", "orjson (>=3.2.1)", "pydantic-extra-types (>=2.0.0)", "pydantic-settings (>=2.0.0)", "python-multipart (>=0.0.5)", "pyyaml (>=5.3.1)", "ujson (>=4.0.1,!=4.0.2,!=4.1.0,!=4.2.0,!=4.3.0,!=5.0.0,!=5.1.0)", "uvicorn[standard] (>=0.12.0)"]
 
+[[package]]
+name = "filelock"
+version = "3.13.1"
+description = "A platform independent file lock."
+optional = false
+python-versions = ">=3.8"
+files = [
+    {file = "filelock-3.13.1-py3-none-any.whl", hash = "sha256:57dbda9b35157b05fb3e58ee91448612eb674172fab98ee235ccb0b5bee19a1c"},
+    {file = "filelock-3.13.1.tar.gz", hash = "sha256:521f5f56c50f8426f5e03ad3b281b490a87ef15bc6c526f168290f0c7148d44e"},
+]
+
+[package.extras]
+docs = ["furo (>=2023.9.10)", "sphinx (>=7.2.6)", "sphinx-autodoc-typehints (>=1.24)"]
+testing = ["covdefaults (>=2.3)", "coverage (>=7.3.2)", "diff-cover (>=8)", "pytest (>=7.4.3)", "pytest-cov (>=4.1)", "pytest-mock (>=3.12)", "pytest-timeout (>=2.2)"]
+typing = ["typing-extensions (>=4.8)"]
+
 [[package]]
 name = "gunicorn"
 version = "21.2.0"
@@ -388,6 +426,20 @@ cli = ["click (==8.*)", "pygments (==2.*)", "rich (>=10,<14)"]
 http2 = ["h2 (>=3,<5)"]
 socks = ["socksio (==1.*)"]
 
+[[package]]
+name = "identify"
+version = "2.5.32"
+description = "File identification library for Python"
+optional = false
+python-versions = ">=3.8"
+files = [
+    {file = "identify-2.5.32-py2.py3-none-any.whl", hash = "sha256:0b7656ef6cba81664b783352c73f8c24b39cf82f926f78f4550eda928e5e0545"},
+    {file = "identify-2.5.32.tar.gz", hash = "sha256:5d9979348ec1a21c768ae07e0a652924538e8bce67313a73cb0f681cf08ba407"},
+]
+
+[package.extras]
+license = ["ukkonen"]
+
 [[package]]
 name = "idna"
 version = "3.6"
@@ -485,6 +537,20 @@ files = [
 packaging = "*"
 sentinels = "*"
 
+[[package]]
+name = "nodeenv"
+version = "1.8.0"
+description = "Node.js virtual environment builder"
+optional = false
+python-versions = ">=2.7,!=3.0.*,!=3.1.*,!=3.2.*,!=3.3.*,!=3.4.*,!=3.5.*,!=3.6.*"
+files = [
+    {file = "nodeenv-1.8.0-py2.py3-none-any.whl", hash = "sha256:df865724bb3c3adc86b3876fa209771517b0cfe596beff01a92700e0e8be4cec"},
+    {file = "nodeenv-1.8.0.tar.gz", hash = "sha256:d51e0c37e64fbf47d017feac3145cdbb58836d7eee8c6f6d3b6880c5456227d2"},
+]
+
+[package.dependencies]
+setuptools = "*"
+
 [[package]]
 name = "numpy"
 version = "1.26.2"
@@ -638,6 +704,24 @@ files = [
 dev = ["pre-commit", "tox"]
 testing = ["pytest", "pytest-benchmark"]
 
+[[package]]
+name = "pre-commit"
+version = "3.5.0"
+description = "A framework for managing and maintaining multi-language pre-commit hooks."
+optional = false
+python-versions = ">=3.8"
+files = [
+    {file = "pre_commit-3.5.0-py2.py3-none-any.whl", hash = "sha256:841dc9aef25daba9a0238cd27984041fa0467b4199fc4852e27950664919f660"},
+    {file = "pre_commit-3.5.0.tar.gz", hash = "sha256:5804465c675b659b0862f07907f96295d490822a450c4c40e747d0b1c6ebcb32"},
+]
+
+[package.dependencies]
+cfgv = ">=2.0.0"
+identify = ">=1.0.0"
+nodeenv = ">=0.11.1"
+pyyaml = ">=5.1"
+virtualenv = ">=20.10.0"
+
 [[package]]
 name = "pydantic"
 version = "1.10.13"
@@ -1004,6 +1088,22 @@ files = [
     {file = "sentinels-1.0.0.tar.gz", hash = "sha256:7be0704d7fe1925e397e92d18669ace2f619c92b5d4eb21a89f31e026f9ff4b1"},
 ]
 
+[[package]]
+name = "setuptools"
+version = "69.0.2"
+description = "Easily download, build, install, upgrade, and uninstall Python packages"
+optional = false
+python-versions = ">=3.8"
+files = [
+    {file = "setuptools-69.0.2-py3-none-any.whl", hash = "sha256:1e8fdff6797d3865f37397be788a4e3cba233608e9b509382a2777d25ebde7f2"},
+    {file = "setuptools-69.0.2.tar.gz", hash = "sha256:735896e78a4742605974de002ac60562d286fa8051a7e2299445e8e8fbb01aa6"},
+]
+
+[package.extras]
+docs = ["furo", "jaraco.packaging (>=9.3)", "jaraco.tidelift (>=1.4)", "pygments-github-lexers (==0.0.5)", "rst.linker (>=1.9)", "sphinx (<7.2.5)", "sphinx (>=3.5)", "sphinx-favicon", "sphinx-inline-tabs", "sphinx-lint", "sphinx-notfound-page (>=1,<2)", "sphinx-reredirects", "sphinxcontrib-towncrier"]
+testing = ["build[virtualenv]", "filelock (>=3.4.0)", "flake8-2020", "ini2toml[lite] (>=0.9)", "jaraco.develop (>=7.21)", "jaraco.envs (>=2.2)", "jaraco.path (>=3.2.0)", "pip (>=19.1)", "pytest (>=6)", "pytest-black (>=0.3.7)", "pytest-checkdocs (>=2.4)", "pytest-cov", "pytest-enabler (>=2.2)", "pytest-mypy (>=0.9.1)", "pytest-perf", "pytest-ruff", "pytest-timeout", "pytest-xdist", "tomli-w (>=1.0.0)", "virtualenv (>=13.0.0)", "wheel"]
+testing-integration = ["build[virtualenv] (>=1.0.3)", "filelock (>=3.4.0)", "jaraco.envs (>=2.2)", "jaraco.path (>=3.2.0)", "packaging (>=23.1)", "pytest", "pytest-enabler", "pytest-xdist", "tomli", "virtualenv (>=13.0.0)", "wheel"]
+
 [[package]]
 name = "six"
 version = "1.16.0"
@@ -1110,7 +1210,27 @@ h11 = ">=0.8"
 [package.extras]
 standard = ["colorama (>=0.4)", "httptools (>=0.5.0)", "python-dotenv (>=0.13)", "pyyaml (>=5.1)", "uvloop (>=0.14.0,!=0.15.0,!=0.15.1)", "watchfiles (>=0.13)", "websockets (>=10.4)"]
 
+[[package]]
+name = "virtualenv"
+version = "20.25.0"
+description = "Virtual Python Environment builder"
+optional = false
+python-versions = ">=3.7"
+files = [
+    {file = "virtualenv-20.25.0-py3-none-any.whl", hash = "sha256:4238949c5ffe6876362d9c0180fc6c3a824a7b12b80604eeb8085f2ed7460de3"},
+    {file = "virtualenv-20.25.0.tar.gz", hash = "sha256:bf51c0d9c7dd63ea8e44086fa1e4fb1093a31e963b86959257378aef020e1f1b"},
+]
+
+[package.dependencies]
+distlib = ">=0.3.7,<1"
+filelock = ">=3.12.2,<4"
+platformdirs = ">=3.9.1,<5"
+
+[package.extras]
+docs = ["furo (>=2023.7.26)", "proselint (>=0.13)", "sphinx (>=7.1.2)", "sphinx-argparse (>=0.4)", "sphinxcontrib-towncrier (>=0.2.1a0)", "towncrier (>=23.6)"]
+test = ["covdefaults (>=2.3)", "coverage (>=7.2.7)", "coverage-enable-subprocess (>=1)", "flaky (>=3.7)", "packaging (>=23.1)", "pytest (>=7.4)", "pytest-env (>=0.8.2)", "pytest-freezer (>=0.4.8)", "pytest-mock (>=3.11.1)", "pytest-randomly (>=3.12)", "pytest-timeout (>=2.1)", "setuptools (>=68)", "time-machine (>=2.10)"]
+
 [metadata]
 lock-version = "2.0"
 python-versions = "^3.11"
-content-hash = "562341ec64732beb741285b0c9687aa792c9a3edb523a842b660a4d3eb3f2ab9"
+content-hash = "4de5d3929a638f2a4f1fabc9b33b9aba8de1bd11dcc8754a0e0b700c3e0632a9"
diff --git a/pyproject.toml b/pyproject.toml
index a0a2555..eebd0fb 100644
--- a/pyproject.toml
+++ b/pyproject.toml
@@ -18,6 +18,7 @@ uvicorn = "^0.24.0.post1"
 pymongo = "^4.6.1"
 mongo-adapter = "^0.3.3"
 httpx = "^0.25.2"
+pre-commit = "^3.5.0"
 
 
 [tool.poetry.group.dev.dependencies]

From c6ecb6e9ab800936bd7e12dca5cec3d27973d562 Mon Sep 17 00:00:00 2001
From: Christian Oertlin <c.oertlin@gmail.com>
Date: Tue, 5 Dec 2023 08:45:18 +0100
Subject: [PATCH 14/15]  remove linting flow tmp

---
 .github/workflows/pull_request_ci.yml | 17 -----------------
 1 file changed, 17 deletions(-)

diff --git a/.github/workflows/pull_request_ci.yml b/.github/workflows/pull_request_ci.yml
index 31d442c..a861b48 100644
--- a/.github/workflows/pull_request_ci.yml
+++ b/.github/workflows/pull_request_ci.yml
@@ -5,23 +5,6 @@ name: Pull Request Actions
 on: [push]
 
 jobs:
-  lint:
-    runs-on: ubuntu-latest
-    steps:
-      - name: Check out git repository
-        uses: actions/checkout@v3
-
-      - name: Set up Python 3.11
-        uses: actions/setup-python@v4
-        with:
-          python-version: "3.11"
-
-      - name: Set up Black
-        uses: psf/black@stable
-        with:
-          options: ". --check --line-length 100"
-          version: "~=23.3.0"
-
   docker-image-push:
     runs-on: ubuntu-latest
     name: Create staging docker image

From af5d84b6c4aa89ece3fd86d45d1c5ed9f616287a Mon Sep 17 00:00:00 2001
From: Christian Oertlin <c.oertlin@gmail.com>
Date: Tue, 5 Dec 2023 09:21:02 +0100
Subject: [PATCH 15/15] fix docker python image

---
 Dockerfile | 4 ++--
 1 file changed, 2 insertions(+), 2 deletions(-)

diff --git a/Dockerfile b/Dockerfile
index 5c553f7..c736032 100644
--- a/Dockerfile
+++ b/Dockerfile
@@ -1,6 +1,6 @@
-FROM python:3.11-slim
+FROM python:3.11-slim-bullseye
 
-LABEL base_image="python:3.11-slim"
+LABEL base_image="python:3.11-slim-bullseye"
 LABEL about.home="https://github.com/Clinical-Genomics/arnold"
 LABEL about.tags="CG Core database and API"