diff --git a/.gitignore b/.gitignore
index 4bf6500..9ec9301 100644
--- a/.gitignore
+++ b/.gitignore
@@ -108,3 +108,6 @@ ENV/
 # VSCode
 .vscode/
 test-reports/
+
+# Gitlab
+vars.env
diff --git a/.gitlab-ci.yml b/.gitlab-ci.yml
new file mode 100644
index 0000000..f5197ad
--- /dev/null
+++ b/.gitlab-ci.yml
@@ -0,0 +1,52 @@
+# To contribute improvements to CI/CD templates, please follow the Development guide at:
+# https://docs.gitlab.com/ee/development/cicd/templates.html
+# This specific template is located at:
+# https://gitlab.com/gitlab-org/gitlab/-/blob/master/lib/gitlab/ci/templates/Python.gitlab-ci.yml
+include:
+  - project: nci-gdc/gitlab-templates
+    ref: master
+    file:
+      - templates/global/full.yaml
+      - templates/python/full.yaml
+
+variables:
+ BASE_CONTAINER_VERSION: "2.0.1"
+ DOCKER_BUILDKIT: 1
+ PIP_EXTRA_INDEX_URL: https://nexus.osdc.io/repository/pypi-all/simple
+ DOCKER_BUILD_OPTS: "--build-arg PIP_EXTRA_INDEX_URL=https://nexus.osdc.io/repository/pypi-all/simple"
+
+tox:
+  image: ${BASE_CONTAINER_REGISTRY}/${REPO_PY_VERSION}-builder:${BASE_CONTAINER_VERSION}
+  before_script:
+    - mkdir -p /usr/share/man/man1
+
+release:
+  image: ${BASE_CONTAINER_REGISTRY}/${REPO_PY_VERSION}-builder:${BASE_CONTAINER_VERSION}
+
+.python_versions:
+  parallel:
+    matrix:
+      - REPO_PY_VERSION: [python3.8]
+
+docker_build:
+  rules:
+    - when: always
+    - if: '$CI_PIPELINE_SOURCE == "schedule"'
+      when: never
+    - if: $CI_COMMIT_REF_NAME == $CI_DEFAULT_BRANCH
+      variables:
+        RELEASE_REGISTRY: containers.osdc.io/ncigdc  # Override globally-defined RELEASE_REGISTRY
+    - if: $CI_COMMIT_REF_NAME =~ /main/
+      variables:
+        RELEASE_REGISTRY: containers.osdc.io/ncigdc
+  script:
+    - echo "docker build ${DOCKER_BUILD_OPTS} -t ${RELEASE_REGISTRY}/$CI_PROJECT_NAME:$VERSION ."
+    - echo "docker push ${DOCKER_PUSH_OPTS} ${RELEASE_REGISTRY}/$CI_PROJECT_NAME:$VERSION"
+    - docker build . 
+      --file ./Dockerfile
+      ${DOCKER_BUILD_OPTS}
+      --build-arg http_proxy
+      --build-arg https_proxy
+      --build-arg BASE_CONTAINER_VERSION
+      -t ${RELEASE_REGISTRY}/${CI_PROJECT_NAME}:${VERSION}
+    - docker push ${DOCKER_PUSH_OPTS} ${RELEASE_REGISTRY}/${CI_PROJECT_NAME}:${VERSION}
diff --git a/.pre-commit-config.yaml b/.pre-commit-config.yaml
index 5b6065d..51c23bc 100644
--- a/.pre-commit-config.yaml
+++ b/.pre-commit-config.yaml
@@ -3,13 +3,13 @@ default_language_version:
   python_venv: python3.8
 
 repos:
-  - repo: git@github.com:Yelp/detect-secrets
-    rev: v1.0.3
+  - repo: https://github.com/Yelp/detect-secrets
+    rev: v1.2.0
     hooks:
       - id: detect-secrets
         args: ['--baseline', '.secrets.baseline']
   - repo: https://github.com/pre-commit/pre-commit-hooks
-    rev: v2.4.0
+    rev: v4.2.0
     hooks:
       - id: check-yaml
       - id: check-toml
@@ -17,18 +17,18 @@ repos:
       - id: detect-aws-credentials
         args: ["--allow-missing-credentials"]
       - id: detect-private-key
+      - id: end-of-file-fixer
   - repo: https://github.com/pycqa/isort
-    rev: 5.8.0
+    rev: 5.10.1
     hooks:
       - id: isort
         name: isort
   - repo: https://github.com/psf/black
-    rev: 20.8b1
+    rev: 22.3.0
     hooks:
       - id: black
   - repo: https://github.com/pycqa/flake8
-    rev: '3.9.2'
+    rev: '4.0.1'
     hooks:
     -   id: flake8
         additional_dependencies: [flake8-docstrings]
-
diff --git a/Dockerfile b/Dockerfile
index 10e3ecd..52b0f9e 100644
--- a/Dockerfile
+++ b/Dockerfile
@@ -1,26 +1,24 @@
-FROM quay.io/ncigdc/python38-builder as builder
+ARG REGISTRY=quay.io
+ARG BASE_CONTAINER_VERSION=2.0.1
+
+FROM ${REGISTRY}/ncigdc/python3.8-builder:${BASE_CONTAINER_VERSION} as builder
 
 COPY ./ /opt
 
 WORKDIR /opt
 
-RUN python -m pip install tox && tox
-
-# tox step builds sdist
+RUN pip install tox && tox -e build
 
-FROM quay.io/ncigdc/python38
+FROM ${REGISTRY}/ncigdc/python3.8:${BASE_CONTAINER_VERSION}
 
 COPY --from=builder /opt/dist/*.tar.gz /opt
-COPY ./requirements.txt /opt/requirements.txt
-
-ENV BINARY=maflib
+COPY requirements.txt /opt
 
 WORKDIR /opt
 
-# Install package from sdist
-RUN pip install -r requirements.txt \
-	&& pip install *.tar.gz \
-	&& rm -rf *.tar.gz requirements.txt
+RUN pip install --no-deps -r requirements.txt \
+	&& pip install --no-deps *.tar.gz \
+	&& rm -f *.tar.gz requirements.txt
 
 ENTRYPOINT ["maflib"]
 
diff --git a/Jenkinsfile b/Jenkinsfile
deleted file mode 100644
index 62e0b85..0000000
--- a/Jenkinsfile
+++ /dev/null
@@ -1,6 +0,0 @@
-#!groovy
-
-library identifier: "jenkins-lib@master"
-bioScriptedLibPipeline {
-  testRunner = 'tox'
-}
diff --git a/MANIFEST.in b/MANIFEST.in
deleted file mode 100644
index 80ac224..0000000
--- a/MANIFEST.in
+++ /dev/null
@@ -1,4 +0,0 @@
-# setuptools_scm includes most files
-exclude .pre-commit-config.yaml
-exclude .secrets.baseline
-exclude .gitignore
diff --git a/Makefile b/Makefile
index ab166aa..017fae8 100644
--- a/Makefile
+++ b/Makefile
@@ -1,40 +1,47 @@
 REPO = maf-lib
+
 MODULE = maflib
 
-GIT_SHORT_HASH:=$(shell git rev-parse --short HEAD)
-GIT_COMMIT_HASH:=$(shell git rev-parse HEAD)
-GIT_DESCRIBE:=$(shell git describe --tags)
+# Redirect error when run in container
+COMMIT_HASH:=$(shell git rev-parse HEAD 2>/dev/null)
+GIT_DESCRIBE:=$(shell git describe --tags 2>/dev/null)
 
 DOCKER_REPO := quay.io/ncigdc
-DOCKER_IMAGE_COMMIT := ${DOCKER_REPO}/${REPO}:${GIT_COMMIT_HASH}
-DOCKER_IMAGE_LATEST := ${DOCKER_REPO}/${REPO}:latest
+DOCKER_IMAGE_COMMIT := ${DOCKER_REPO}/${REPO}:${COMMIT_HASH}
 DOCKER_IMAGE_DESCRIBE := ${DOCKER_REPO}/${REPO}:${GIT_DESCRIBE}
+DOCKER_IMAGE_LATEST := ${DOCKER_REPO}/${REPO}:latest
+
+# Env args
+PIP_EXTRA_INDEX_URL ?=
+http_proxy ?=
+https_proxy ?=
+REGISTRY ?= quay.io
 
-TWINE_REPOSITORY_URL?=""
 
 .PHONY: version version-*
 version:
-	@python setup.py --version
+	@tox -e version
 
 version-docker:
-	@echo ${DOCKER_IMAGE_COMMIT}
-
-version-docker-tag:
-	@echo
+	@echo ${DOCKER_IMAGE_DESCRIBE}
 
 .PHONY: docker-login
 docker-login:
 	docker login -u="${QUAY_USERNAME}" -p="${QUAY_PASSWORD}" quay.io
 
+.PHONY: venv
+venv:
+	@echo
+	rm -rf .venv/
+	tox -r -e dev --devenv .venv
 
 .PHONY: init init-*
 init: init-pip init-hooks
-
-init-pip:
+init-pip: init-venv
 	@echo
 	@echo -- Installing pip packages --
 	pip-sync requirements.txt dev-requirements.txt
-	python setup.py develop
+	python -m pip install -e .
 
 init-hooks:
 	@echo
@@ -47,69 +54,66 @@ init-venv:
 
 .PHONY: clean clean-*
 clean: clean-dirs
-
 clean-dirs:
 	rm -rf ./build/
 	rm -rf ./dist/
 	rm -rf ./*.egg-info/
-	rm -rf ./.tox/
-	rm -rf ./htmlcov
-
-clean-docker:
-	@docker rmi -f ${DOCKER_IMAGE_COMMIT}
+	rm -rf ./test-reports/
+	rm -rf ./htmlcov/
+	rm -rf coverage.xml
+	rm -rf .coverage
 
 .PHONY: requirements requirements-*
 requirements: init-venv requirements-prod requirements-dev
-
-requirements-prod:
-	pip-compile -o requirements.txt
-
 requirements-dev:
 	pip-compile -o dev-requirements.txt dev-requirements.in
 
+requirements-prod:
+	pip-compile -o requirements.txt pyproject.toml
+
 .PHONY: build build-*
 
 build: build-docker
 
 build-docker: clean
+	@echo
 	@echo -- Building docker --
-	docker build . -f Dockerfile \
-		--build-arg http_proxy=${PROXY} \
-		--build-arg https_proxy=${PROXY} \
+	docker build . \
+		--file ./Dockerfile \
+		--build-arg http_proxy \
+		--build-arg https_proxy \
+		--build-arg REGISTRY \
 		-t "${DOCKER_IMAGE_COMMIT}" \
-		-t "${DOCKER_IMAGE_LATEST}"
+		-t "${DOCKER_IMAGE_DESCRIBE}" \
+		-t "${REPO}"
 
 build-pypi: clean
-	@tox -e check_dist
+	@echo
+	tox -e build
 
 .PHONY: lint test test-* tox
 test: tox
+lint:
+	@echo
+	@echo -- Lint --
+	tox -p -e flake8
 
 test-unit:
-	@echo
-	@echo -- Unit Test --
-	tox -e py36
+	tox -e py3
 
 test-docker:
 	@echo
 
 tox:
-	@echo Running tox
-	tox -p all
-
-lint:
 	@echo
-	@echo -- Lint --
-	tox -p -e flake8
+	TOX_PARALLEL_NO_SPINNER=1 tox -p --recreate
 
 .PHONY: publish-*
 publish-docker:
-	docker tag ${DOCKER_IMAGE_LATEST} ${DOCKER_IMAGE_DESCRIBE}
 	docker push ${DOCKER_IMAGE_COMMIT}
 	docker push ${DOCKER_IMAGE_DESCRIBE}
 
 publish-pypi:
 	@echo
-	@echo Publishing dists
-	@python3 -m pip install --user --upgrade twine
+	@echo Publishing wheel
 	python3 -m twine upload dist/*
diff --git a/dev-requirements.in b/dev-requirements.in
index f30c805..25efff2 100644
--- a/dev-requirements.in
+++ b/dev-requirements.in
@@ -1,5 +1,5 @@
 -c requirements.txt
-detect-secrets==1.0.3
+detect-secrets==1.2.0
 isort
 flake8
 flake8-docstrings
diff --git a/dev-requirements.txt b/dev-requirements.txt
index 7376909..32e950c 100644
--- a/dev-requirements.txt
+++ b/dev-requirements.txt
@@ -4,6 +4,8 @@
 #
 #    pip-compile --output-file=dev-requirements.txt dev-requirements.in
 #
+--extra-index-url https://nexus.osdc.io/repository/pypi-all/simple
+
 appdirs==1.4.4
     # via virtualenv
 attrs==20.2.0
@@ -16,7 +18,7 @@ chardet==4.0.0
     # via requests
 coverage==5.3
     # via pytest-cov
-detect-secrets==1.0.3
+detect-secrets==1.2.0
     # via -r dev-requirements.in
 distlib==0.3.1
     # via virtualenv
diff --git a/maflib/column_types.py b/maflib/column_types.py
index 4e0dc3e..46cc66f 100644
--- a/maflib/column_types.py
+++ b/maflib/column_types.py
@@ -101,7 +101,7 @@ def __validate__(self) -> Optional[str]:
 
 
 class StringColumn(NullableStringColumn):
-    """ A column where the value must be a non-empty string"""
+    """A column where the value must be a non-empty string"""
 
     EmptyStringMessage = "Empty string is not allowed"
 
diff --git a/maflib/record.py b/maflib/record.py
index 72f2a32..65c8a99 100644
--- a/maflib/record.py
+++ b/maflib/record.py
@@ -256,7 +256,7 @@ def value(self, key: TKey) -> Any:
             return None
 
     def column_values(self) -> List[Optional[Any]]:
-        """Gets the values for all columns in order. """
+        """Gets the values for all columns in order."""
         return [
             (column.value if column is not None else None) for column in self.values()
         ]
diff --git a/maflib/validation.py b/maflib/validation.py
index fee18b1..6ce0691 100644
--- a/maflib/validation.py
+++ b/maflib/validation.py
@@ -82,7 +82,7 @@ def __str__(self) -> str:
 
 
 class MafValidationError:
-    """Stores a specific validation error and type """
+    """Stores a specific validation error and type"""
 
     __IgnoringMessageFormat = "Ignoring MAF validation error: %s"
 
diff --git a/pyproject.toml b/pyproject.toml
index 34deae0..8886152 100644
--- a/pyproject.toml
+++ b/pyproject.toml
@@ -1,13 +1,56 @@
 [build-system]
-requires = ["setuptools>=45", "wheel", "setuptools_scm[toml]>=6.2"]
-build-backend = "setuptools.build_meta"
+requires = ["flit_scm"]
+build-backend = "flit_scm:buildapi"
+
+[project]
+name = "bioinf-maflib"
+description = "Library for creating and reading MAF files"
+authors = [
+    {name = "Charles Czysz", email = "czysz@uchicago.edu"}
+]
+
+readme = "README.md"
+requires-python = ">=3.8"
+license = {file = "LICENSE"}
+classifiers = [
+    "License :: OSI Approved :: Apache Software License",
+	"Programming Language :: Python :: 3",
+	"Programming Language :: Python :: 3 :: Only"
+]
+dynamic = ["version"]
+dependencies = []
+
+[project.urls]
+homepage = "https://github.com/NCI-GDC/maf-lib"
+
+[project.scripts]
+maflib = "maflib.__main__:main"
 
 [tool.setuptools_scm]
-local_scheme = "dirty-tag"
-version_scheme = "release-branch-semver"
 write_to = "maflib/_version.py"
+local_scheme = "dirty-tag"
+version_scheme = "python-simplified-semver"
 fallback_version = "0"
 
+[tool.coverage.run]
+source = ["maflib"]
+branch = true
+parallel = true
+
+[tool.flit.module]
+name = "maflib"
+
+[tool.flit.sdist]
+include = ["maflib/_version.py"]
+exclude = [
+        ".*",
+        "dev-requirements.*",
+        "Dockerfile",
+        "Jenkinsfile",
+        "*travis.yml",
+        "tox.ini",
+]
+
 [tool.black]
 line-length = 88
 skip-string-normalization = true
@@ -25,3 +68,6 @@ python_version = 3.8
 disallow_untyped_defs = true
 warn_return_any = true
 warn_unused_configs = true
+
+[tool.coverage.report]
+show_missing = true
diff --git a/requirements.txt b/requirements.txt
index 271db3b..3736d0b 100644
--- a/requirements.txt
+++ b/requirements.txt
@@ -2,5 +2,6 @@
 # This file is autogenerated by pip-compile with python 3.8
 # To update, run:
 #
-#    pip-compile --output-file=requirements.txt
+#    pip-compile --output-file=requirements.txt pyproject.toml
 #
+--extra-index-url https://nexus.osdc.io/repository/pypi-all/simple
diff --git a/setup.cfg b/setup.cfg
deleted file mode 100644
index fdbe74f..0000000
--- a/setup.cfg
+++ /dev/null
@@ -1,25 +0,0 @@
-[metadata]
-name = bioinf_maflib
-description = Maflib
-url = https://github.com/NCI-GDC/maf-lib
-author = Charles Czysz
-author_email = czysz@uchicago.edu
-python_requires = >=3.8
-license_files =
-	LICENSE
-long_description = file:README.md
-long_description_content_type = text/markdown
-classifiers =
-	Programming Language :: Python :: 3
-	Programming Language :: Python :: 3 :: Only
-
-[options]
-install_requires =
-
-zip_safe = False
-include_package_data = True
-packages = find:
-
-[options.entry_points]
-console_scripts =
-	maflib = maflib.__main__:main
diff --git a/setup.py b/setup.py
deleted file mode 100644
index f205a47..0000000
--- a/setup.py
+++ /dev/null
@@ -1,10 +0,0 @@
-#!/usr/bin/env python
-
-from setuptools import setup
-
-setup(
-    use_scm_version=True,
-    setup_requires=['setuptools_scm'],
-)
-
-# __END__
diff --git a/tox.ini b/tox.ini
index 8cd249b..6447fbf 100644
--- a/tox.ini
+++ b/tox.ini
@@ -1,58 +1,118 @@
 [tox]
-envlist = py38,flake8,check_dist,type
-isolated_build = True
+envlist = py3,help,version,flake8,type,cov
+isolated_build = true
 
-[flake8]
-ignore = C901,D100,D104,E501,E302,E502,E126,E731,F841,W503,W605
-extend_ignore = D tests/
-exclude =
-        .tox,
-        .git,
-        .direnv,
-        __pycache__,
-        build,
-        dist,
-        *.pyc,
-        *.egg-info,
-        .eggs
-docstring-convention=google
+[tox:.package]
+basepython = python3
 
 [testenv]
+setenv = 
+	package = maflib
+	PYTHONHASHSEED = 0
+passenv = PIP_EXTRA_INDEX_URL
+skip_install =
+	false
+install_command = python -m pip install {opts} {packages}
+deps = 
+	-rdev-requirements.txt
+	-rrequirements.txt
+commands = pytest -vv {posargs}
+
+[testenv:dev]
+basepython = python3.8
+
+[testenv:requirements]
+deps = pip-tools
+skip_install =
+	true
+commands =
+  pip-compile -o dev-requirements.txt dev-requirements.in
+
+[testenv:help]
+skip_install =
+	false
 deps = 
 	-rdev-requirements.txt
 	-rrequirements.txt
 commands =
-	pytest -lvv \
-	--cov-report=term-missing \
-	--cov-report=html \
-	--junitxml=test-reports/results.xml \
-	--cov=maflib \
-	tests/
+	python -m {env:package} --help
+
+[testenv:cov]
+skip_install=True
+deps = 
+	-rdev-requirements.txt
+	-rrequirements.txt
+commands =
+	coverage run -m pytest tests/
+	coverage combine
+	coverage report -m
+	coverage xml
+	coverage xml -o test-reports/results.xml
 
 [testenv:flake8]
-skip_install = true
+skip_install=True
+deps = 
+	-rdev-requirements.txt
+	-rrequirements.txt
+commands = 
+	flake8 {env:package}/ tests/
+
+[testenv:type]
+skip_install = false
 deps=
-    flake8
+	-rrequirements.txt
+	-rdev-requirements.txt
 commands =
-    flake8 maflib/ tests/ setup.py
+	python -m mypy {env:package}/
+
+[testenv:build]
+skip_install= true
+isolated_build = false
+install_command = python -m pip install {opts} {packages}
+deps= 
+  flit
+  setuptools_scm
+commands = 
+  python -m setuptools_scm
+  python -m flit build
 
-[testenv:check_dist]
-skip_install = true
+[testenv:publish]
+isolated_build=False
+skip_install=true
+passenv =
+	TWINE_USERNAME
+	TWINE_PASSWORD
+	TWINE_REPOSITORY_URL
+install_command = python -m pip install {opts} {packages}
 deps= 
-	setuptools_scm
-	wheel
+  setuptools_scm
+  flit
 	twine
-whitelist_externals = rm
 commands = 
-	python setup.py -q clean --all
-	python setup.py -q egg_info
-	python setup.py -q sdist --formats gztar bdist_wheel
-	twine check dist/*
+  python -m setuptools_scm
+  python -m flit build
+  twine check dist/*
+  twine upload dist/*
 
-[testenv:type]
-skip_install = true
-deps=
-        mypy
-commands =
-        python -m mypy maflib/
+[testenv:version]
+skip_install=True
+allowlist_externals =
+  git
+deps =
+commands = 
+  git describe --tags
 
+[flake8]
+ignore = C901,D100,D104,E501,E302,E502,E126,E731,F841,W503,W605
+extend_ignore = D tests/
+exclude = 
+	.tox,
+	.git,
+	.direnv,
+	__pycache__,
+	build,
+	dist,
+	*.pyc,
+	*.egg-info,
+	.eggs
+docstring-convention=google