Replace old config files with modern pyproject.toml

.flake8

@@ -0,0 +1,28 @@
+[flake8]
+exclude =
+    __init__.py
+    __main__.py
+
+max-line-length = 80
+ignore =
+    # whitespace before ':'
+    E203
+    # too many leading '#' for block comment
+    E266
+    # line too long
+    E501
+    # line break before binary operator
+    W503
+select =
+    # mccabe complexity
+    C
+    # pycodestyle
+    E
+    # pyflakes error
+    F
+    # pyflakes warning
+    W
+    # bugbear
+    B
+    # line exceeds max-line-length + 10%
+    B950

.github/workflows/lint-test-cov.yml

@@ -26,9 +26,9 @@ jobs:
     - name: Install dependencies
       run: |
         python -m pip install --upgrade pip
-        pip install flake8 codecov pytest pytest-flake8 pytest-cov
+        pip install flake8 pytest pytest-flake8 pytest-cov
         pip install -r requirements-dev.txt
         pip install -e .
-    - name: Lint, testing and coverage with pytest
+    - name: Testing and coverage with pytest
       run: |
         pytest

pyproject.toml

@@ -0,0 +1,28 @@
+[build-system]
+requires = ["setuptools"]
+build-backend = "setuptools.build_meta"
+
+[tool.distutils.bdist_wheel]
+universal = true
+
+[tool.coverage.run]
+source = ["cooler"]
+
+omit = [
+    "cooler/__main__.py",
+    "cooler/_version.py",
+    "cooler/sandbox/*",
+    "cooler/cli/csort.py"
+]
+
+[tool.coverage.report]
+exclude_lines = [
+    "pragma: no cover",
+    "return NotImplemented",
+    "raise NotImplementedError"
+]
+
+[tool.pytest.ini_options]
+addopts = "--cov cooler --cov-config .coveragerc --cov-report term-missing --cov-report html --cov-report=xml"
+filterwarnings = ["ignore::PendingDeprecationWarning"]
+testpaths = ["tests"]

requirements-dev.txt

@@ -1,5 +1,6 @@
 -r requirements.txt
 biopython
+coverage[toml]
 dask[array,dataframe]
 ipytree
 matplotlib