diff --git a/.devcontainer/devcontainer.json b/.devcontainer/devcontainer.json
new file mode 100644
index 0000000..186ec08
--- /dev/null
+++ b/.devcontainer/devcontainer.json
@@ -0,0 +1,75 @@
+// For format details, see https://aka.ms/devcontainer.json. For config options, see the
+// README at: https://github.com/devcontainers/templates/tree/main/src/ubuntu
+{
+	"image": "python:3.10-slim",
+	"features": {
+		"ghcr.io/devcontainers/features/git:1": {
+			"ppa": true,
+			"version": "latest"
+		},
+		"ghcr.io/va-h/devcontainers-features/uv:1": {
+			"shellautocompletion": true,
+			"version": "latest"
+		},
+		"ghcr.io/jsburckhardt/devcontainer-features/ruff:1": {},
+		"ghcr.io/itsmechlark/features/redis-server:1": {
+			"version": "latest"
+		}
+	},
+	"updateRemoteUserUID": true,
+	"containerEnv": {
+		"WORKON_HOME": "${containerWorkspaceFolder}/.venv",
+		"PYTHONPATH": "${containerWorkspaceFolder}"
+	},
+	"onCreateCommand": {
+		"update apt": [
+			"/usr/bin/apt",
+			"update"
+		],
+		"sync venv/install if missing": [
+			"/usr/local/bin/uv",
+			"sync",
+			"--frozen"
+		]
+	},
+	"postCreateCommand": {
+		"install ssh client": [
+			"/usr/bin/apt",
+			"install",
+			"--no-install-recommends",
+			"-y",
+			"openssh-client"
+		]
+	},
+	"postAttachCommand": {
+		"message": [
+			"/usr/bin/echo",
+			"Sleeping while environment activates"
+		],
+		"sleep": [
+			"/usr/bin/sleep",
+			"10s"
+		]
+	},
+	"customizations": {
+		"vscode": {
+			"extensions": [
+				"ms-python.python",
+				"ryanluker.vscode-coverage-gutters",
+				"ms-azuretools.vscode-docker",
+				"ms-python.isort",
+				"matangover.mypy",
+				"davidanson.vscode-markdownlint",
+				"ms-vscode.vscode-typescript-next",
+				"charliermarsh.ruff",
+				"tamasfe.even-better-toml",
+				"mechatroner.rainbow-csv"
+			],
+			"settings": {
+				"python.terminal.activateEnvironment": true,
+				"python.terminal.activateEnvInCurrentTerminal": true,
+				"python.venvPath": "${containerWorkspaceFolder}"
+			}
+		}
+	}
+}
diff --git a/.github/workflows/python.yml b/.github/workflows/python.yml
index d4adf3c..763c17d 100644
--- a/.github/workflows/python.yml
+++ b/.github/workflows/python.yml
@@ -22,7 +22,7 @@ jobs:
       fail-fast: false
       matrix:
         os: [ubuntu-latest]
-        python-version: ["3.7", "3.8", "3.9", "3.10", "3.11.0-beta.5 - 3.11"]
+        python-version: ["3.10", "3.11", "3.12"]
 
     steps:
       - uses: actions/checkout@v3
@@ -32,20 +32,29 @@ jobs:
         with:
           python-version: ${{ matrix.python-version }}
 
-      - name: Install Hatch
-        run: pip install --upgrade hatch
+      - name: Install dependencies
+        run:
+          - apt update && apt install yamllint
+          - pip install uv
 
-      - name: Run tests
-        run: hatch run ci-report
-
-      - name: Upload coverage data
-        uses: actions/upload-artifact@v3
-        with:
-          name: coverage-data
-          path: coverage.xml
+      - name: Check code
+        run:
+          - yamllint .
+          - uv run mypy --check .
+          - uv run ruff check .
 
-      - name: Publish Test Report
-        uses: mikepenz/action-junit-report@v3
-        if: success() || failure()
-        with:
-          report_paths: unit_test.xml
+      - name: Run tests
+        run: uv run pytest --junitxml=pytest.xml
+
+      # TODO: Look into github actions, these are out of date
+      # - name: Upload coverage data
+      #   uses: actions/upload-artifact@v3
+      #   with:
+      #     name: coverage-data
+      #     path: coverage.xml
+
+      # - name: Publish Test Report
+      #   uses: mikepenz/action-junit-report@v3
+      #   if: success() || failure()
+      #   with:
+      #     report_paths: unit_test.xml
diff --git a/.gitlab-ci.yml b/.gitlab-ci.yml
index b7007b1..d96a1e2 100644
--- a/.gitlab-ci.yml
+++ b/.gitlab-ci.yml
@@ -1,12 +1,13 @@
 ---
 variables:
+  JUNIT_TEST_REPORT: test_report_${CI_COMMIT_SHORT_SHA}.html
+  COVERAGE_TEST_REPORT: coverage_report_${CI_COMMIT_SHORT_SHA}
   PYTHON_VERSION:
-    value: "3.8"
+    value: "3.10"
     options:
-      - "3.8"
-      - "3.9"
       - "3.10"
       - "3.11"
+      - "3.12"
     description: Python version to use
 
 stages:
@@ -26,13 +27,21 @@ validate-yaml:
         - "*.yml"
         - "*.yaml"
 
-Check-For-Black:
+.python:
+  image:
+    name: python:${PYTHON_VERSION}-slim
+    pull_policy: if-not-present
+  before_script:
+    - pip install uv
+  allow_failure: false
+
+Code-Check:
+  extends: .python
   stage: validate
-  image: black
   script:
     - cd $CI_PROJECT_DIR
-    - black --check src/
-  allow_failure: false
+    - uv run mypy --check .
+    - uv run ruff check .
   rules:
     - if: $CI_JOB_MANUAL
     - if: $CI_PIPELINE_SOURCE == 'merge_request_event'
@@ -42,15 +51,14 @@ Check-For-Black:
 
 Check-HLA-Modified-Dates:
   stage: validate
-  image: python:${PYTHON_VERSION}-slim
-  before_script:
+  extends: .python
+  variables:
+    PYTHONPATH: "${CI_BUILDS_DIR}/src"
+  script:
     - apt update
     - apt install git-restore-mtime -y --no-install-recommends
-    - pip install typer
-  script:
     - cd $CI_PROJECT_DIR
-    - python tools/check_date_modified.py check-dates
-  allow_failure: false
+    - uv run tools/check_date_modified.py check-dates
   rules:
     - if: $CI_JOB_MANUAL
     - if: $CI_PIPELINE_SOURCE == 'merge_request_event'
@@ -59,23 +67,31 @@ Check-HLA-Modified-Dates:
         - src/**/*.mtime
 
 Unit-Tests:
-  image: python:${PYTHON_VERSION}-slim
-  before_script:
-    - pip install hatch
+  extends: .python
+  stage: test
   script:
-    - hatch env run --env test ci-report
+    - cd $CI_PROJECT_DIR
+    - uv run pytest
+      -vra
+      --html=${JUNIT_TEST_REPORT}
+      --self-contained-html
+      --cov-report=html:${COVERAGE_TEST_REPORT}
+      --cov-report=term
+      --junitxml=pytest.xml
   parallel:
     matrix:
       - PYTHON_VERSION:
-          - "3.8"
-          - "3.9"
           - "3.10"
           - "3.11"
+          - "3.12"
   coverage: '/^TOTAL.+?(\d+\%)$/'
   interruptible: true
   artifacts:
     reports:
-      junit: unit_test.xml
+      junit: pytest.xml
       coverage_report:
         coverage_format: cobertura
         path: coverage.xml
+    paths:
+      - ${COVERAGE_TEST_REPORT}/*
+      - ${JUNIT_TEST_REPORT}
diff --git a/.pre-commit-config.yaml b/.pre-commit-config.yaml
index 173f6fe..53d3985 100644
--- a/.pre-commit-config.yaml
+++ b/.pre-commit-config.yaml
@@ -9,7 +9,12 @@ repos:
       - id: end-of-file-fixer
       - id: name-tests-test
       - id: trailing-whitespace
-  - repo: https://github.com/psf/black
-    rev: 23.1.0
+  - repo: https://github.com/astral-sh/ruff-pre-commit
+    # Ruff version.
+    rev: v0.9.9
     hooks:
-      - id: black
+      # Run the linter.
+      - id: ruff
+        args: [--fix]
+      # Run the formatter.
+      - id: ruff-format
diff --git a/.vscode/extensions.json b/.vscode/extensions.json
new file mode 100755
index 0000000..885a358
--- /dev/null
+++ b/.vscode/extensions.json
@@ -0,0 +1,14 @@
+{
+    "recommendations": [
+        "ms-python.python",
+        "ryanluker.vscode-coverage-gutters",
+        "ms-azuretools.vscode-docker",
+        "ms-python.isort",
+        "matangover.mypy",
+        "davidanson.vscode-markdownlint",
+        "ms-vscode.vscode-typescript-next",
+        "charliermarsh.ruff",
+        "tamasfe.even-better-toml",
+        "mechatroner.rainbow-csv"
+    ],
+}
diff --git a/.vscode/settings.json b/.vscode/settings.json
new file mode 100755
index 0000000..d01aa1d
--- /dev/null
+++ b/.vscode/settings.json
@@ -0,0 +1,47 @@
+{
+    "[python]": {
+        "diffEditor.ignoreTrimWhitespace": true,
+        "editor.detectIndentation": false,
+        "editor.tabSize": 4,
+        "editor.wordBasedSuggestions": "off",
+        "gitlens.codeLens.symbolScopes": [
+            "!Module"
+        ],
+        "editor.codeActionsOnSave": {
+            "source.organizeImports.ruff": "always"
+        },
+        "editor.formatOnSave": true,
+        "editor.defaultFormatter": "charliermarsh.ruff"
+    },
+    "editor.renderControlCharacters": true,
+    "editor.renderFinalNewline": "dimmed",
+    "editor.renderWhitespace": "none",
+    "editor.rulers": [
+        80,
+        110
+    ],
+    "files.associations": {
+        "*.env": "properties"
+    },
+    "files.encoding": "utf8",
+    "files.eol": "\n",
+    "files.insertFinalNewline": true,
+    "files.trimFinalNewlines": true,
+    "files.trimTrailingWhitespace": true,
+    "python.envFile": "${workspaceFolder}/.env",
+    "python.languageServer": "Default",
+    "python.terminal.activateEnvironment": true,
+    "python.testing.autoTestDiscoverOnSaveEnabled": true,
+    "python.testing.pytestArgs": [
+        "tests"
+    ],
+    "python.testing.pytestEnabled": true,
+    "python.testing.unittestEnabled": false,
+    "search.exclude": {
+        "**/.pytest_cache": false,
+        "**/.venv": false,
+        "**/__pycache__": false,
+        "**/output": false
+    },
+    "testing.gutterEnabled": true
+}
diff --git a/.yamllint.yml b/.yamllint.yml
new file mode 100644
index 0000000..8e49526
--- /dev/null
+++ b/.yamllint.yml
@@ -0,0 +1,11 @@
+ignore:
+  - .git/*
+  - .venv/*
+
+extends: default
+
+rules:
+  truthy:
+    ignore: .github/*
+  document-end: disable
+  document-start: disable
diff --git a/Pipfile b/Pipfile
deleted file mode 100644
index be4e313..0000000
--- a/Pipfile
+++ /dev/null
@@ -1,26 +0,0 @@
-[[source]]
-url = "https://pypi.org/simple"
-verify_ssl = true
-name = "pypi"
-
-[packages]
-biopython = "*"
-numpy = "*"
-pydantic = "*"
-pydantic-numpy = "*"
-typer = "*"
-pytz = "*"
-
-[dev-packages]
-pytest = "*"
-mypy = "*"
-mypy-extensions = "*"
-isort = "*"
-black = "*"
-pytest-cov = "*"
-pytest-html = "*"
-pytest-mock = "*"
-pytest-xdist = "*"
-
-[requires]
-python_version = "3.10"
diff --git a/Pipfile.lock b/Pipfile.lock
deleted file mode 100644
index 3a98bbc..0000000
--- a/Pipfile.lock
+++ /dev/null
@@ -1,637 +0,0 @@
-{
-    "_meta": {
-        "hash": {
-            "sha256": "b5446a4785ef5d52f244e5312f3c970af691d08be85bc5e0848b22f123910bf2"
-        },
-        "pipfile-spec": 6,
-        "requires": {
-            "python_version": "3.10"
-        },
-        "sources": [
-            {
-                "name": "pypi",
-                "url": "https://pypi.org/simple",
-                "verify_ssl": true
-            }
-        ]
-    },
-    "default": {
-        "annotated-types": {
-            "hashes": [
-                "sha256:47cdc3490d9ac1506ce92c7aaa76c579dc3509ff11e098fc867e5130ab7be802",
-                "sha256:58da39888f92c276ad970249761ebea80ba544b77acddaa1a4d6cf78287d45fd"
-            ],
-            "markers": "python_version >= '3.7'",
-            "version": "==0.5.0"
-        },
-        "biopython": {
-            "hashes": [
-                "sha256:11d673698b3d0d6589292ea951fb62cb24ea27d273eca0d08dbbd956690f97f5",
-                "sha256:2cf38112b6d8415ad39d6a611988cd11fb5f33eb09346666a87263beba9614e0",
-                "sha256:2f9cfaf16d55ab80d514e7aebe5710dabe4e4ff47ede851031202e33b3249da3",
-                "sha256:35506e39822c52d11cf09a3951e82375ca1bb9303960b4286acf02c9a6f6c4cc",
-                "sha256:3b36ba1bf6395c09a365c53530c9d71f3617763fa2c1d452b3d8948368c0f1de",
-                "sha256:655df416936662c0c8a06a549cb25e1560e1fea5067d850f34fb714b8a3fae6c",
-                "sha256:65b93b513ce9dd7b2ce058720eadf42cd03f312db3409356efeb93123d1320aa",
-                "sha256:6ebfbce0d91796c7aef422ee9dffe8827e07e5abaa94545e006f1f20e965c80b",
-                "sha256:762c6c43a8486b5fcd07f136a3217b87d24755618b9ea9da1f17124ff44c2ad6",
-                "sha256:793c42a376cd63f62f8a088ce39b7dc6b5c55e4e9031d887c434de1595bfa4b8",
-                "sha256:7a168709694e10b338718c18d967edd5b56c237dc88642c22275796007a70000",
-                "sha256:7c5c07123ff5f44c9e6b5369df854a38afd3c0c50ef58498a0ae8f7eb799f3e8",
-                "sha256:811796f8d222aa3869a50e31e54ce62b69106b47cd8bb06934867c0d843297b5",
-                "sha256:8bb0c690c7368f255ed45236bf0f5464b476b8c083c8f634533921af78278261",
-                "sha256:919a2c583cabf9c96d2ae4e1245a6b0376932fb342aca302a0fc198b71ab3275",
-                "sha256:97cbdbed01b2512471f36c74b91658d1dfbdcbf39bc038f6ce5a41c3e60a8fc6",
-                "sha256:9ba33244f0eff830beaa7240065bdb5095d96fded6599b76bbb9ddab45cd2bbd",
-                "sha256:a51d9c1d1b4b634447535da74a644fae59bc234fbbf9001e2dc6b6fbabb98019",
-                "sha256:b09efcb4733c8770f25eab5fe555a96a08f5ab9e1bc36939e08ebf2ffbf3e0f1",
-                "sha256:b37c0d24191e5c96ca02415a5188551980c83a0d518bbc4ffe3c9a5d1fe0ee81",
-                "sha256:ccd729249fd5f586dd4c2a3507c2ea2456825d7e615e97c07c409c850eaf4594",
-                "sha256:e41b55edcfd448630e77bf4de66a7235324a8a149621499891da6bd1d5085b9a",
-                "sha256:ee51bb1cd7decffd24da6b76d5e01b7e2fd818ab85cf0c180226cbb5793a3abd",
-                "sha256:ef7c79b65b0b3f3c7dc59e20a7f8ae5758d8e852cb8b9cace590dc5617e348ba"
-            ],
-            "index": "pypi",
-            "version": "==1.81"
-        },
-        "click": {
-            "hashes": [
-                "sha256:48ee849951919527a045bfe3bf7baa8a959c423134e1a5b98c05c20ba75a1cbd",
-                "sha256:fa244bb30b3b5ee2cae3da8f55c9e5e0c0e86093306301fb418eb9dc40fbded5"
-            ],
-            "markers": "python_version >= '3.7'",
-            "version": "==8.1.6"
-        },
-        "compress-pickle": {
-            "extras": [
-                "lz4"
-            ],
-            "hashes": [
-                "sha256:3e944ce0eeab5b6331324d62351c957d41c9327c8417d439843e88fe69b77991",
-                "sha256:598650da4686d9bd97bee185b61e74d7fe1872bb0c23909d5ed2d8793b4a8818"
-            ],
-            "markers": "python_version >= '3.6'",
-            "version": "==2.1.0"
-        },
-        "lz4": {
-            "hashes": [
-                "sha256:0ca83a623c449295bafad745dcd399cea4c55b16b13ed8cfea30963b004016c9",
-                "sha256:0f5614d8229b33d4a97cb527db2a1ac81308c6e796e7bdb5d1309127289f69d5",
-                "sha256:1c4c100d99eed7c08d4e8852dd11e7d1ec47a3340f49e3a96f8dfbba17ffb300",
-                "sha256:1f25eb322eeb24068bb7647cae2b0732b71e5c639e4e4026db57618dcd8279f0",
-                "sha256:200d05777d61ba1ff8d29cb51c534a162ea0b4fe6d3c28be3571a0a48ff36080",
-                "sha256:31d72731c4ac6ebdce57cd9a5cabe0aecba229c4f31ba3e2c64ae52eee3fdb1c",
-                "sha256:3a85b430138882f82f354135b98c320dafb96fc8fe4656573d95ab05de9eb092",
-                "sha256:4931ab28a0d1c133104613e74eec1b8bb1f52403faabe4f47f93008785c0b929",
-                "sha256:4caedeb19e3ede6c7a178968b800f910db6503cb4cb1e9cc9221157572139b49",
-                "sha256:65d5c93f8badacfa0456b660285e394e65023ef8071142e0dcbd4762166e1be0",
-                "sha256:6b50f096a6a25f3b2edca05aa626ce39979d63c3b160687c8c6d50ac3943d0ba",
-                "sha256:7211dc8f636ca625abc3d4fb9ab74e5444b92df4f8d58ec83c8868a2b0ff643d",
-                "sha256:7a9eec24ec7d8c99aab54de91b4a5a149559ed5b3097cf30249b665689b3d402",
-                "sha256:7c2df117def1589fba1327dceee51c5c2176a2b5a7040b45e84185ce0c08b6a3",
-                "sha256:7e2dc1bd88b60fa09b9b37f08553f45dc2b770c52a5996ea52b2b40f25445676",
-                "sha256:83903fe6db92db0be101acedc677aa41a490b561567fe1b3fe68695b2110326c",
-                "sha256:83acfacab3a1a7ab9694333bcb7950fbeb0be21660d236fd09c8337a50817897",
-                "sha256:86480f14a188c37cb1416cdabacfb4e42f7a5eab20a737dac9c4b1c227f3b822",
-                "sha256:867664d9ca9bdfce840ac96d46cd8838c9ae891e859eb98ce82fcdf0e103a947",
-                "sha256:8df16c9a2377bdc01e01e6de5a6e4bbc66ddf007a6b045688e285d7d9d61d1c9",
-                "sha256:8f00a9ba98f6364cadda366ae6469b7b3568c0cced27e16a47ddf6b774169270",
-                "sha256:926b26db87ec8822cf1870efc3d04d06062730ec3279bbbd33ba47a6c0a5c673",
-                "sha256:a6a46889325fd60b8a6b62ffc61588ec500a1883db32cddee9903edfba0b7584",
-                "sha256:a98b61e504fb69f99117b188e60b71e3c94469295571492a6468c1acd63c37ba",
-                "sha256:ad38dc6a7eea6f6b8b642aaa0683253288b0460b70cab3216838747163fb774d",
-                "sha256:b10b77dc2e6b1daa2f11e241141ab8285c42b4ed13a8642495620416279cc5b2",
-                "sha256:d5ea0e788dc7e2311989b78cae7accf75a580827b4d96bbaf06c7e5a03989bd5",
-                "sha256:e05afefc4529e97c08e65ef92432e5f5225c0bb21ad89dee1e06a882f91d7f5e",
-                "sha256:e1431d84a9cfb23e6773e72078ce8e65cad6745816d4cbf9ae67da5ea419acda",
-                "sha256:ec6755cacf83f0c5588d28abb40a1ac1643f2ff2115481089264c7630236618a",
-                "sha256:edc2fb3463d5d9338ccf13eb512aab61937be50aa70734bcf873f2f493801d3b",
-                "sha256:edd8987d8415b5dad25e797043936d91535017237f72fa456601be1479386c92",
-                "sha256:edda4fb109439b7f3f58ed6bede59694bc631c4b69c041112b1b7dc727fffb23",
-                "sha256:f571eab7fec554d3b1db0d666bdc2ad85c81f4b8cb08906c4c59a8cad75e6e22",
-                "sha256:f7c50542b4ddceb74ab4f8b3435327a0861f06257ca501d59067a6a482535a77"
-            ],
-            "version": "==4.3.2"
-        },
-        "numpy": {
-            "hashes": [
-                "sha256:0d60fbae8e0019865fc4784745814cff1c421df5afee233db6d88ab4f14655a2",
-                "sha256:1a1329e26f46230bf77b02cc19e900db9b52f398d6722ca853349a782d4cff55",
-                "sha256:1b9735c27cea5d995496f46a8b1cd7b408b3f34b6d50459d9ac8fe3a20cc17bf",
-                "sha256:2792d23d62ec51e50ce4d4b7d73de8f67a2fd3ea710dcbc8563a51a03fb07b01",
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-        "pytest-metadata": {
-            "hashes": [
-                "sha256:769a9c65d2884bd583bc626b0ace77ad15dbe02dd91a9106d47fd46d9c2569ca",
-                "sha256:a17b1e40080401dc23177599208c52228df463db191c1a573ccdffacd885e190"
-            ],
-            "markers": "python_version >= '3.7'",
-            "version": "==3.0.0"
-        },
-        "pytest-mock": {
-            "hashes": [
-                "sha256:21c279fff83d70763b05f8874cc9cfb3fcacd6d354247a976f9529d19f9acf39",
-                "sha256:7f6b125602ac6d743e523ae0bfa71e1a697a2f5534064528c6ff84c2f7c2fc7f"
-            ],
-            "index": "pypi",
-            "version": "==3.11.1"
-        },
-        "pytest-xdist": {
-            "hashes": [
-                "sha256:d5ee0520eb1b7bcca50a60a518ab7a7707992812c578198f8b44fdfac78e8c93",
-                "sha256:ff9daa7793569e6a68544850fd3927cd257cc03a7ef76c95e86915355e82b5f2"
-            ],
-            "index": "pypi",
-            "version": "==3.3.1"
-        },
-        "tomli": {
-            "hashes": [
-                "sha256:939de3e7a6161af0c887ef91b7d41a53e7c5a1ca976325f429cb46ea9bc30ecc",
-                "sha256:de526c12914f0c550d15924c62d72abc48d6fe7364aa87328337a31007fe8a4f"
-            ],
-            "markers": "python_version < '3.11'",
-            "version": "==2.0.1"
-        },
-        "typing-extensions": {
-            "hashes": [
-                "sha256:440d5dd3af93b060174bf433bccd69b0babc3b15b1a8dca43789fd7f61514b36",
-                "sha256:b75ddc264f0ba5615db7ba217daeb99701ad295353c45f9e95963337ceeeffb2"
-            ],
-            "markers": "python_version >= '3.7'",
-            "version": "==4.7.1"
-        }
-    }
-}
diff --git a/mypy.ini b/mypy.ini
deleted file mode 100644
index f6c95b6..0000000
--- a/mypy.ini
+++ /dev/null
@@ -1,5 +0,0 @@
-[mypy]
-
-#[mypy-Bio.*]
-ignore_missing_imports = True
-plugins = numpy.typing.mypy_plugin
diff --git a/pyproject.toml b/pyproject.toml
index 2f692aa..41ed3a9 100644
--- a/pyproject.toml
+++ b/pyproject.toml
@@ -10,7 +10,7 @@ requires-python = ">=3.10"
 license = "MIT"
 keywords = []
 authors = [
-  { name = "Rosemary ?", email = "retired@bccfe.ca" },
+  { name = "Rosemary McCloskey", email = "retired@bccfe.ca" },
   { name = "David Rickett", email = "drickett@bccfe.ca" },
 ]
 classifiers = [
@@ -18,19 +18,36 @@ classifiers = [
   "Programming Language :: Python",
   "Programming Language :: Python :: 3.10",
   "Programming Language :: Python :: 3.11",
+  "Programming Language :: Python :: 3.12",
   "Programming Language :: Python :: Implementation :: CPython",
   "Programming Language :: Python :: Implementation :: PyPy",
 ]
+
+dynamic = ["version"]
 dependencies = [
-  "biopython",
-  "pydantic",
-  "pydantic-numpy",
-  "typer",
-  "pytz",
-  "numpy",
+  "biopython>=1.85",
+  "numpy>=2.2.3",
+  "pydantic>=2.10.6",
+  "pydantic-numpy>=8.0.1",
+  "pytz>=2025.1",
+  "typer>=0.15.2",
 ]
 
-dynamic = ["version"]
+[dependency-groups]
+dev = [
+  "mypy>=1.15.0",
+  "mypy-extensions>=1.0.0",
+  "pandas>=2.2.3",
+  "pandas-stubs>=2.2.3.241126",
+  "pre-commit>=4.1.0",
+  "pytest>=8.3.5",
+  "pytest-cov>=6.0.0",
+  "pytest-html>=4.1.1",
+  "pytest-mock>=3.14.0",
+  "pytest-xdist>=3.6.1",
+  "ruff>=0.9.9",
+  "types-pytz>=2025.1.0.20250204",
+]
 
 [project.urls]
 Documentation = "https://github.com/unknown/easyhla#readme"
@@ -61,53 +78,13 @@ directory = "output"
 [tool.hatch.build.targets.wheel]
 packages = ["src/easyhla"]
 
-[tool.hatch.envs.default]
-dependencies = [
-  "biopython",
-  "pydantic",
-  "pydantic-numpy",
-  "typer",
-  "pytz",
-  "numpy",
-]
-
-[tool.hatch.envs.test]
-template = "default"
-extra-dependencies = [
-  "pytest",
-  "pytest-cov",
-  "pytest-html",
-  "pytest-mock",
-  "pytest-xdist",
-]
-
-[tool.hatch.envs.dev]
-template = "test"
-extra-dependencies = [
-  "pytest",
-  "pytest-cov",
-  "pytest-html",
-  "pytest-mock",
-  "pytest-xdist",
-  "black",
-  "mypy-extensions",
-  "isort",
-]
-
-[tool.hatch.envs.test.scripts]
-cov = "pytest --cov-report=term-missing --cov-config=pyproject.toml --cov=src/easyhla --cov=tests {args}"
-cov-report = "pytest --cov-report xml --cov-config=pyproject.toml --cov=src/easyhla --cov=tests {args}"
-ci-report = "pytest --junitxml=unit_test.xml --cov-report xml:coverage.xml --cov-report term --cov-config=pyproject.toml --cov=src/easyhla --cov=tests {args}"
-full-report = "pytest --junitxml=unit_test.xml --html=easyhla_test_report.html --self-contained-html --cov-report xml:coverage.xml --cov-report term --cov-report html --cov-config=pyproject.toml --cov=src/easyhla --cov=tests {args}"
-no-cov = "cov --no-cov {args}"
-
-[[tool.hatch.envs.test.matrix]]
-python = ["310", "311"]
+[tool.uv]
+package = true
 
 [tool.pytest.ini_options]
 pythonpath = "src"
 minversion = "6.0"
-addopts = "-ra -n 4 --cov --cov-report xml --strict-markers -m 'not slow'"
+addopts = "-ra -n 4 --cov --cov-report term --cov-report xml --strict-markers -m 'not slow'"
 testpaths = ["tests"]
 markers = [
   "integration: Run integration tests",
@@ -117,6 +94,7 @@ markers = [
 [tool.coverage.run]
 branch = true
 parallel = true
+source = ["src"]
 omit = [
   "src/easyhla/__init__.py",
   "src/easyhla/__about__.py",
@@ -127,6 +105,27 @@ omit = [
 
 [tool.coverage.report]
 exclude_lines = ["no cov", "if __name__ == .__main__.:", "if TYPE_CHECKING:"]
+skip_empty = true
+
+[tool.coverage.xml]
+output = 'coverage.xml'
+
+[tool.ruff]
+target-version = "py312"
+
+[tool.ruff.format]
+quote-style = "double"
+
+[tool.ruff.lint]
+select = ["E4", "E7", "E9", "F", "C"]
+# ignore warnings where `== True` occurs, because we're using a lot of pandas
+# https://www.flake8rules.com/rules/E712.html
+ignore = ["E712"]
+
 
 [tool.pydocstyle]
 match = "src/**/*.py"
+
+[tool.mypy]
+plugins = ["numpy.typing.mypy_plugin"]
+ignore_missing_imports = true
diff --git a/src/easyhla/__init__.py b/src/easyhla/__init__.py
index e73df81..a613319 100644
--- a/src/easyhla/__init__.py
+++ b/src/easyhla/__init__.py
@@ -1,2 +1,3 @@
-from .easyhla import EasyHLA, HLAType
-from .entrypoint import run
+from .easyhla import EasyHLA as EasyHLA
+from .easyhla import HLAType as HLAType
+from .entrypoint import run as run
diff --git a/src/easyhla/easyhla.py b/src/easyhla/easyhla.py
index 33baee0..6e6843e 100644
--- a/src/easyhla/easyhla.py
+++ b/src/easyhla/easyhla.py
@@ -1,14 +1,15 @@
+# ruff: noqa: C901
+# TODO: Remove this noqa line and refactor/reduce code-complexity
+
 import logging
 import os
 import re
 from datetime import datetime
 from enum import Enum
-from pathlib import Path
 from typing import Any, Dict, Final, List, Literal, Optional, Tuple
 
 import Bio.SeqIO
 import numpy as np
-import typer
 
 from .models import (
     Alleles,
@@ -342,7 +343,7 @@ def combine_stds(
         seq: List[int],
         max_mismatch_threshold: Optional[int],
     ) -> Dict[int, List[HLACombinedStandardResult]]:
-        length = len(matching_stds[0].sequence)
+        # length = len(matching_stds[0].sequence)
 
         default_min = 9999
         if max_mismatch_threshold is None:
@@ -376,9 +377,9 @@ def combine_stds(
                         computed_minimum_mismatches = max(
                             mismatches, tmp_max_mismatch_threshold
                         )
-                    if not mismatches in combos:
+                    if mismatches not in combos:
                         combos[mismatches] = {}
-                    if not combined_std_name in combos[mismatches]:
+                    if combined_std_name not in combos[mismatches]:
                         combos[mismatches][combined_std_name] = []
                     stds = [std_a.allele, std_b.allele]
                     stds.sort()
@@ -423,11 +424,11 @@ def load_hla_frequencies(self, letter: HLA_TYPES) -> Dict[str, int]:
         with open(filepath, "r", encoding="utf-8") as f:
             for line in f.readlines():
                 column_id = EasyHLA.COLUMN_IDS[letter]
-                l = line.strip().split(",")[column_id : column_id + 2]
-                _l = ",".join([f"{a[:2]}|{a[-2:]}" for a in l])
-                if hla_freqs.get(_l, None) is None:
-                    hla_freqs[_l] = 0
-                hla_freqs[_l] += 1
+                line_array = line.strip().split(",")[column_id : column_id + 2]
+                elements = ",".join([f"{a[:2]}|{a[-2:]}" for a in line_array])
+                if hla_freqs.get(elements, None) is None:
+                    hla_freqs[elements] = 0
+                hla_freqs[elements] += 1
         return hla_freqs
 
     # TODO: Convert this to a dictionary instead of a object that looks like:
@@ -449,9 +450,9 @@ def load_hla_stds(self, letter: HLA_TYPES) -> List[HLAStandard]:
 
         with open(filepath, "r", encoding="utf-8") as f:
             for line in f.readlines():
-                l = line.strip().split(",")
-                seq = self.nuc2bin((l[1] + l[2]))
-                hla_stds.append(HLAStandard(allele=l[0], sequence=seq))
+                line_array = line.strip().split(",")
+                seq = self.nuc2bin((line_array[1] + line_array[2]))
+                hla_stds.append(HLAStandard(allele=line_array[0], sequence=seq))
         return hla_stds
 
     def load_allele_definitions_last_modified_time(self) -> datetime:
@@ -497,7 +498,7 @@ def interpret(
                 return None
             if not self.check_bases(str(entry.seq), samp):
                 return None
-        except ValueError as e:
+        except ValueError:
             return None
 
         is_exon = False
@@ -551,7 +552,9 @@ def interpret(
             seq = np.concatenate((exon2_bin, exon3_bin))
         else:
             seq = self.pad_short(
-                self.nuc2bin(entry.seq), samp, hla_std=self.hla_stds[0]
+                self.nuc2bin(entry.seq),  # type: ignore
+                samp,
+                hla_std=self.hla_stds[0],
             )
             exon2 = self.bin2nuc(seq[: EasyHLA.EXON2_LENGTH])
             intron = self.bin2nuc(seq[EasyHLA.EXON2_LENGTH : -EasyHLA.EXON3_LENGTH])
@@ -616,7 +619,7 @@ def interpret(
             alleles_all_str=alleles_all_str,
             ambig=int(ambig),
             homozygous=int(homozygous),
-            mismatch_count=f"{mismatch_count}",
+            mismatch_count=mismatch_count,
             mismatches=f"{mismatches}",
             exon2=exon2.upper(),
             intron=intron.upper(),
@@ -691,7 +694,7 @@ def run(
             f"{npats} patients, {nseqs} sequences processed.", to_stdout=to_stdout
         )
 
-        self.log.info(f"% patients, % sequences processed.", npats, nseqs)
+        self.log.info("% patients, % sequences processed.", npats, nseqs)
 
         with open(output_filename, "w", encoding="utf-8") as f:
             f.write(
@@ -814,9 +817,9 @@ def get_mismatches(
             _seq = np.array([int(nuc) for nuc in hla_csr.standard.split("-")])
             # TODO: replace with https://stackoverflow.com/questions/16094563/numpy-get-index-where-value-is-true
             for idx in np.flatnonzero(_seq ^ seq):
-                if not idx in correct_bases_at_pos:
+                if idx not in correct_bases_at_pos:
                     correct_bases_at_pos[idx] = []
-                if not _seq[idx] in correct_bases_at_pos[idx]:
+                if _seq[idx] not in correct_bases_at_pos[idx]:
                     correct_bases_at_pos[idx].append(_seq[idx])
 
         mislist: List[str] = []
diff --git a/src/easyhla/entrypoint.py b/src/easyhla/entrypoint.py
index 93ccf1d..2fd34e1 100644
--- a/src/easyhla/entrypoint.py
+++ b/src/easyhla/entrypoint.py
@@ -28,8 +28,6 @@ def main(
         "--print",
         "-p",
         help="Print to stdout as sequences are interpretted",
-        flag_value=True,
-        is_flag=True,
     ),
     sequence_file: Path = typer.Argument(
         ...,
@@ -57,8 +55,8 @@ def main(
 
     easyhla.run(
         easyhla.letter,
-        sequence_file,
-        output_file,
+        sequence_file.as_posix(),
+        output_file.as_posix(),
         threshold=mismatch_threshold,
         to_stdout=print_to_stdout,
     )
diff --git a/src/easyhla/models.py b/src/easyhla/models.py
index bd228ec..f2377ea 100644
--- a/src/easyhla/models.py
+++ b/src/easyhla/models.py
@@ -1,5 +1,5 @@
 import re
-from typing import Dict, List, Optional, Set, Tuple
+from typing import Dict, List, Set, Tuple
 
 import numpy as np
 import pydantic_numpy.typing as pnd
@@ -28,7 +28,7 @@ def is_homozygous(self) -> bool:
         :return: ...
         :rtype: bool
         """
-        return any([_a[0] == _a[1] for _a in self.alleles])
+        return any(_a[0] == _a[1] for _a in self.alleles)
 
     def is_ambiguous(self) -> bool:
         """
@@ -108,7 +108,7 @@ def stringify_clean(self) -> str:
         clean_allele: List[str] = []
         for n in [0, 1]:
             for i in [4, 3, 2, 1]:
-                if len(set([":".join(a[n][0:i]) for a in self.get_collection()])) == 1:
+                if len({":".join(a[n][0:i]) for a in self.get_collection()}) == 1:
                     clean_allele.append(
                         re.sub(
                             r"[A-Z]$", "", ":".join(self.get_collection()[0][n][0:i])
@@ -151,7 +151,7 @@ class HLAStandard(NumpyModel):
     sequence: pnd.NpNDArray
 
     def __eq__(self, other):
-        if type(self) != type(other):
+        if not isinstance(other, self.__class__):
             raise TypeError(f"Cannot compare against {type(other)}")
         return all(
             [self.allele == other.allele, np.array_equal(self.sequence, other.sequence)]
@@ -162,7 +162,7 @@ class HLAStandardMatch(HLAStandard):
     mismatch: int
 
     def __eq__(self, other):
-        if type(other) != type(self):
+        if not isinstance(other, self.__class__):
             raise TypeError(f"Cannot compare against {type(other)}")
         return all(
             [
@@ -205,7 +205,7 @@ def get_result(self) -> List[str]:
         ]
 
     def get_result_as_str(self) -> str:
-        return ",".join([el for el in self.get_result()])
+        return ",".join(el for el in self.get_result())
 
 
 class HLAResult(BaseModel):
diff --git a/tests/conftest.py b/tests/conftest.py
index 557aecf..0b301ec 100644
--- a/tests/conftest.py
+++ b/tests/conftest.py
@@ -30,8 +30,8 @@ def make_comparison(easyhla: EasyHLA, ref_seq: str, test_seq: str) -> str:
             side_is_short = "test"
         elif len(ref) < len(test):
             side_is_short = "ref"
-        return easyhla.bin2nuc(masked_seq) + f" [{side_is_short} is short]"
-    return easyhla.bin2nuc(masked_seq)
+        return easyhla.bin2nuc(masked_seq) + f" [{side_is_short} is short]"  # type: ignore
+    return easyhla.bin2nuc(masked_seq)  # type: ignore
 
 
 def compare_ref_vs_test(
@@ -60,9 +60,9 @@ def compare_ref_vs_test(
 
     column_names = reference_file[0].strip().split(",")
 
-    assert len(reference_file) == len(
-        test_output_file
-    ), "Size of test output does not match reference file!"
+    assert len(reference_file) == len(test_output_file), (
+        "Size of test output does not match reference file!"
+    )
 
     for row_num, (ref, test) in enumerate(zip(reference_file, test_output_file)):
         try:
@@ -86,19 +86,19 @@ def compare_ref_vs_test(
 
                 _row_num = row_num + 1 + int(skip_preamble[1])
                 # Check that there is no strippable whitespace when there shouldn't be.
-                assert (
-                    _test == _test.strip()
-                ), f"Whitespace detected at row {_row_num}, column {col_num} ('{column_names[col_num]}')"
-                assert (
-                    _ref == _ref.strip()
-                ), f"[REFERENCE FILE] Whitespace detected at row {_row_num}, column {col_num} ('{column_names[col_num]}')"
-
-                assert len(_ref.strip()) == len(
-                    _test.strip()
-                ), f"Length mismatch detected at row {_row_num}, column {col_num} ('{column_names[col_num]}')"
-                assert (
-                    _ref.strip() == _test.strip()
-                ), f"Content mismatch detected at row {_row_num}, column {col_num} ('{column_names[col_num]}')"
+                assert _test == _test.strip(), (
+                    f"Whitespace detected at row {_row_num}, column {col_num} ('{column_names[col_num]}')"
+                )
+                assert _ref == _ref.strip(), (
+                    f"[REFERENCE FILE] Whitespace detected at row {_row_num}, column {col_num} ('{column_names[col_num]}')"
+                )
+
+                assert len(_ref.strip()) == len(_test.strip()), (
+                    f"Length mismatch detected at row {_row_num}, column {col_num} ('{column_names[col_num]}')"
+                )
+                assert _ref.strip() == _test.strip(), (
+                    f"Content mismatch detected at row {_row_num}, column {col_num} ('{column_names[col_num]}')"
+                )
 
                 if row_num > 0 and column_names[col_num] in [
                     "ALLELES_CLEAN",
@@ -107,7 +107,9 @@ def compare_ref_vs_test(
                     assert (
                         set(_ref.strip().split(";")) ^ set(_test.strip().split(";"))
                         == set()
-                    ), f"Order mismatch detected at row {_row_num}, column {col_num} ('{column_names[col_num]}')"
+                    ), (
+                        f"Order mismatch detected at row {_row_num}, column {col_num} ('{column_names[col_num]}')"
+                    )
         except AssertionError as e:
             print("REF >>>", ref)
             print("OUT >>>", test)
diff --git a/tests/easyhla_test.py b/tests/easyhla_test.py
index a6de352..3b77c52 100644
--- a/tests/easyhla_test.py
+++ b/tests/easyhla_test.py
@@ -1,9 +1,7 @@
-import json
 import os
-from contextlib import nullcontext as does_not_raise
 from datetime import datetime
 from pathlib import Path
-from typing import Any, Dict, List, Optional, Tuple
+from typing import Dict, List, Tuple
 
 import numpy as np
 import pytest
@@ -17,7 +15,7 @@
     HLAStandardMatch,
 )
 
-from .conftest import compare_ref_vs_test, make_comparison
+from .conftest import compare_ref_vs_test
 
 
 @pytest.fixture(scope="module")
@@ -71,14 +69,14 @@ def test_unknown_hla_type(self):
         Assert we raise a value error if we put in an unknown HLA type.
         """
         with pytest.raises(ValueError):
-            easyhla = EasyHLA("D")
+            _ = EasyHLA("D")  # type: ignore[arg-type]
 
     def test_known_hla_type_lowercase(self):
         """
         Assert we raise a value error if we put in an HLA type with wrong case.
         """
         with pytest.raises(ValueError):
-            easyhla = EasyHLA("a")
+            _ = EasyHLA("a")  # type: ignore[arg-type]
 
     @pytest.mark.parametrize("easyhla", ["A"], indirect=True)
     def test_load_allele_definitions_last_modified_time(
@@ -650,7 +648,7 @@ def test_get_matching_stds(
         hla_stds: List[HLAStandard],
         exp_result: List[HLAStandardMatch],
     ):
-        result = easyhla.get_matching_stds(seq=sequence, hla_stds=hla_stds)
+        result = easyhla.get_matching_stds(seq=sequence, hla_stds=hla_stds)  # type: ignore
         print(result)
         assert result == exp_result
 
@@ -1036,7 +1034,7 @@ def test_combine_stds(
         sequence: List[int],
         threshold: int,
         matching_standards: List[HLAStandardMatch],
-        exp_result: List[int],
+        exp_result: Dict[int, List[int]],
     ):
         result = easyhla.combine_stds(
             matching_stds=matching_standards,
@@ -1044,8 +1042,8 @@ def test_combine_stds(
             max_mismatch_threshold=threshold,
         )
         print(sorted(result.items()))
-        print([(k, v) for k, v in exp_result.items()])
-        assert sorted(result.items()) == [(k, v) for k, v in exp_result.items()]
+        print((k, v) for k, v in exp_result.items())
+        assert sorted(result.items()) == list((k, v) for k, v in exp_result.items())  # noqa: C400
 
     @pytest.mark.parametrize(
         "best_matches, exp_homozygous, exp_alleles",
@@ -1167,10 +1165,10 @@ def test_run(self, easyhla: EasyHLA):
 
         print(f"Test ended at {end_compare_time.isoformat()}")
 
-        print(f"Time elapsed: {(end_compare_time-start_time).total_seconds()}")
+        print(f"Time elapsed: {(end_compare_time - start_time).total_seconds()}")
         print(
-            f"Time elapsed for interpretation: {(end_time-start_time).total_seconds()}"
+            f"Time elapsed for interpretation: {(end_time - start_time).total_seconds()}"
         )
         print(
-            f"Time elapsed for output comparison: {(end_compare_time-end_time).total_seconds()}"
+            f"Time elapsed for output comparison: {(end_compare_time - end_time).total_seconds()}"
         )
diff --git a/tests/models_test.py b/tests/models_test.py
index 6dded62..b48ecf3 100644
--- a/tests/models_test.py
+++ b/tests/models_test.py
@@ -1,13 +1,9 @@
-from typing import Dict, List, Set, Tuple
+from typing import List, Set, Tuple
 
 import pytest
 
-from easyhla.easyhla import DATE_FORMAT, EasyHLA
 from easyhla.models import (
     Alleles,
-    HLACombinedStandardResult,
-    HLAStandard,
-    HLAStandardMatch,
 )
 
 
diff --git a/tools/check_date_modified.py b/tools/check_date_modified.py
index ea29c0d..15db82e 100644
--- a/tools/check_date_modified.py
+++ b/tools/check_date_modified.py
@@ -17,15 +17,13 @@
 file.
 """
 
-
 import os
 from datetime import datetime
-from math import ceil
 from typing import List, Tuple
 
 import typer
 
-from src.easyhla.easyhla import DATE_FORMAT
+from easyhla.easyhla import DATE_FORMAT
 
 app = typer.Typer()
 
@@ -133,8 +131,8 @@ def _check_dates() -> bool:
 def check_dates():
     if not _check_dates():
         warning_msg = "WARNING: The last modified file date has changed!"
-        preamble_height = 4
-        len_msg = ceil(len(warning_msg) / preamble_height)
+        # preamble_height = 4
+        # len_msg = ceil(len(warning_msg) / preamble_height)
         print("#" * len(warning_msg))
         print("#" * len(warning_msg))
         # if you want a silly message on an angle, uncomment this.
diff --git a/tools/data_parse.py b/tools/data_parse.py
index 747d8a5..ee31ba9 100644
--- a/tools/data_parse.py
+++ b/tools/data_parse.py
@@ -34,10 +34,9 @@
 
 # 0-1, percentage of input samples that should be suffixed '_exon#'
 # HLA Type A has to include the intron
+perc_pure_exon: float = 0.0
 if HLA_TYPE.upper() == "A":
-    perc_pure_exon: float = 0.0
-else:
-    perc_pure_exon: float = 0.0
+    perc_pure_exon = 0.0
 
 sample_input_df = df[[ENUM_IDENTIFIER[HLA_TYPE], "EXON2", "INTRON", "EXON3"]]
 sample_input_seqs: Dict[str, str] = {}
@@ -47,21 +46,21 @@
     chance = Random().random()
     if chance > perc_pure_exon and row[1]["INTRON"] != "":
         if HLA_TYPE == "A":
-            sample_input_seqs[
-                row[1][ENUM_IDENTIFIER[HLA_TYPE]]
-            ] = f"{row[1]['EXON2']}{row[1]['INTRON']}{row[1]['EXON3']}"
+            sample_input_seqs[row[1][ENUM_IDENTIFIER[HLA_TYPE]]] = (
+                f"{row[1]['EXON2']}{row[1]['INTRON']}{row[1]['EXON3']}"
+            )
         else:
-            sample_input_seqs[
-                row[1][ENUM_IDENTIFIER[HLA_TYPE]]
-            ] = f"{row[1]['EXON2']}{row[1]['EXON3']}"
+            sample_input_seqs[row[1][ENUM_IDENTIFIER[HLA_TYPE]]] = (
+                f"{row[1]['EXON2']}{row[1]['EXON3']}"
+            )
     else:
         pure_exon_samples.append(row[1][ENUM_IDENTIFIER[HLA_TYPE]])
-        sample_input_seqs[
-            row[1][ENUM_IDENTIFIER[HLA_TYPE]] + "_exon2"
-        ] = f"{row[1]['EXON2']}"
-        sample_input_seqs[
-            row[1][ENUM_IDENTIFIER[HLA_TYPE]] + "_exon3"
-        ] = f"{row[1]['EXON3']}"
+        sample_input_seqs[row[1][ENUM_IDENTIFIER[HLA_TYPE]] + "_exon2"] = (
+            f"{row[1]['EXON2']}"
+        )
+        sample_input_seqs[row[1][ENUM_IDENTIFIER[HLA_TYPE]] + "_exon3"] = (
+            f"{row[1]['EXON3']}"
+        )
 
 with open(
     os.path.join(
@@ -98,7 +97,7 @@
                 row[1][ENUM_IDENTIFIER[HLA_TYPE]] in pure_exon_samples
                 and col == "INTRON"
             ):
-                f.write(f",")
+                f.write(",")
             elif col == output_columns[-1]:
                 f.write(f"{row[1][col]}")
             else:
diff --git a/tools/manual_comparison.py b/tools/manual_comparison.py
index 6da82f6..aaeac13 100644
--- a/tools/manual_comparison.py
+++ b/tools/manual_comparison.py
@@ -1,15 +1,17 @@
+# ruff: noqa: C901
+
 """
 Perform a manual comparison between two output files.
 
 For help use `python tests/manual_comparison.py --help`.
 """
 
-import os
+from itertools import zip_longest
 
 import typer
 
-from src.easyhla.easyhla import EasyHLA
-from tests.conftest import compare_ref_vs_test, make_comparison
+from easyhla.easyhla import EasyHLA
+from tests.conftest import make_comparison
 
 
 def main(
@@ -30,22 +32,16 @@ def main(
         False,
         "--skip-preamble",
         "-s",
-        is_flag=True,
-        flag_value=True,
         help="If both files begin with a timestamp, skip that line",
     ),
     skip_preamble_ref: bool = typer.Option(
         False,
         "--skip-preamble-ref",
-        is_flag=True,
-        flag_value=True,
         help="If reference file begins with a timestamp, skip that line",
     ),
     skip_preamble_out: bool = typer.Option(
         False,
         "--skip-preamble-output",
-        is_flag=True,
-        flag_value=True,
         help="If output file begins with a timestamp, skip that line",
     ),
 ) -> None:
@@ -60,7 +56,7 @@ def main(
     )
 
     with open(ref_output_file, "r", encoding="utf-8") as f_reference:
-        reference_file = f_reference.readlines()[int(_skip_preamble[0]) :]
+        reference_file = "\n".join(f_reference.readlines()[int(_skip_preamble[0]) :])
     with open(output_file, "r", encoding="utf-8") as f_test_output:
         test_output_file = f_test_output.readlines()[int(_skip_preamble[1]) :]
 
@@ -68,11 +64,13 @@ def main(
     if len(column_names) <= 1:
         raise RuntimeError("No column names detected, you may need to specify -s!")
 
-    assert len(reference_file) == len(
-        test_output_file
-    ), "Size of test output does not match reference file!"
+    assert len(reference_file) == len(test_output_file), (
+        "Size of test output does not match reference file!"
+    )
 
-    for row_num, (ref, test) in enumerate(zip(reference_file, test_output_file)):
+    for row_num, (ref, test) in enumerate(
+        zip_longest(reference_file, test_output_file)
+    ):
         for col_num, (_ref, _test) in enumerate(
             zip(ref.strip().split(","), test.strip().split(","))
         ):
diff --git a/uv.lock b/uv.lock
new file mode 100644
index 0000000..ce30eb0
--- /dev/null
+++ b/uv.lock
@@ -0,0 +1,1092 @@
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+requires-python = ">=3.10"
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