From ccc07b8e6e8e9a5f297ba03743ebd2b84cfa523f Mon Sep 17 00:00:00 2001
From: Chaim Halbert <chaim.leib.halbert@gmail.com>
Date: Tue, 11 Mar 2025 14:25:01 -0700
Subject: [PATCH 01/17] feat(ci): test with GitHub Actions

---
 .github/workflows/build.yml  |  45 ++++++++++++
 .github/workflows/manual.yml |  47 ------------
 Dockerfile                   | 137 -----------------------------------
 README.md                    |   2 +-
 pyproject.toml               |  44 +++++++++++
 scripts/testall.sh           |  15 ----
 6 files changed, 90 insertions(+), 200 deletions(-)
 create mode 100644 .github/workflows/build.yml
 delete mode 100644 .github/workflows/manual.yml
 delete mode 100644 Dockerfile
 create mode 100644 pyproject.toml
 delete mode 100755 scripts/testall.sh

diff --git a/.github/workflows/build.yml b/.github/workflows/build.yml
new file mode 100644
index 0000000..7ddb206
--- /dev/null
+++ b/.github/workflows/build.yml
@@ -0,0 +1,45 @@
+# This workflow will install Python dependencies, run tests and lint with a single version of Python
+# For more information see: https://docs.github.com/en/actions/automating-builds-and-tests/building-and-testing-python
+
+name: build
+
+on:
+  push:
+    branches: [ "master", "gha" ]
+  pull_request:
+    branches: [ "master" ]
+
+permissions:
+  contents: read
+
+jobs:
+  build:
+
+    runs-on: ubuntu-latest
+    strategy:
+      matrix:
+        python-version: ["3.9", "3.10", "3.11", "3.12", "3.13"]
+
+    steps:
+    - uses: actions/checkout@v4
+    - name: Set up Python ${{ matrix.python-version }}
+      uses: actions/setup-python@v5
+      with:
+        python-version: ${{ matrix.python-version }}
+    - name: Display Python verison
+      run: python -c "import sys; print(sys.version)"
+    - name: Install dependencies
+      run: |
+        python -m pip install --upgrade pip
+        pip install flake8 pytest pytest-cov sortedcontainers
+        if [ -f requirements.txt ]; then pip install -r requirements.txt; fi
+    - name: Lint with flake8
+      run: |
+        # stop the build if there are Python syntax errors or undefined names
+        flake8 . --count --select=E9,F63,F7,F82 --show-source --statistics
+        # exit-zero treats all errors as warnings. The GitHub editor is 127 chars wide
+        flake8 . --count --exit-zero --max-complexity=10 --max-line-length=127 --statistics
+    - name: Test with pytest
+      run: |
+        pytest
+
diff --git a/.github/workflows/manual.yml b/.github/workflows/manual.yml
deleted file mode 100644
index ee9f72b..0000000
--- a/.github/workflows/manual.yml
+++ /dev/null
@@ -1,47 +0,0 @@
-name: ci
-
-on:
-  push:
-    branches:
-      - "master"
-
-env:
-  TEST_TAG: ${{ secrets.DOCKERHUB_USERNAME }}/intervaltree:test
-  LATEST_TAG: ${{ secrets.DOCKERHUB_USERNAME }}/intervaltree:latest
-
-jobs:
-  build:
-    runs-on: ubuntu-latest
-    steps:
-      -
-        name: Checkout
-        uses: actions/checkout@v3
-      -
-        name: Login to Docker Hub
-        uses: docker/login-action@v2
-        with:
-          username: ${{ secrets.DOCKERHUB_USERNAME }}
-          password: ${{ secrets.DOCKERHUB_TOKEN }}
-      -
-        name: Set up Docker Buildx
-        uses: docker/setup-buildx-action@v2
-      -
-        name: Build and export to Docker
-        uses: docker/build-push-action@v4
-        with:
-          context: .
-          file: ./Dockerfile
-          load: true
-          tags: ${{ env.TEST_TAG }}
-      -
-        name: Test
-        run: docker run --rm ${{ env.TEST_TAG }}
-      -
-        name: Build and push
-        uses: docker/build-push-action@v4
-        with:
-          context: .
-          file: ./Dockerfile
-          push: true
-          tags: ${{ env.LATEST_TAG }}
-
diff --git a/Dockerfile b/Dockerfile
deleted file mode 100644
index 1b7e32a..0000000
--- a/Dockerfile
+++ /dev/null
@@ -1,137 +0,0 @@
-# Modified by chaimleib March 2023 from
-#   https://github.com/vicamo/docker-pyenv/blob/main/alpine/Dockerfile
-#
-# Changes:
-# * customize the versions of python installed
-# * remove the dependency on github.com/momo-lab/xxenv-latest
-# * forbid failures when building python
-# * add other tools like parallel
-# * run intervaltree tests
-
-FROM alpine:latest AS base
-
-ENV PYENV_ROOT="/opt/pyenv"
-ENV PYENV_SHELL="bash"
-ENV PATH="${PYENV_ROOT}/shims:${PYENV_ROOT}/bin:$PATH"
-
-# http://bugs.python.org/issue19846
-# > At the moment, setting "LANG=C" on a Linux system *fundamentally breaks Python 3*, and that's not OK.
-ENV LANG C.UTF-8
-
-# runtime dependencies
-RUN set -eux; \
-    apk update; \
-    apk add --no-cache \
-        bash \
-        build-base \
-        bzip2 \
-        ca-certificates \
-        curl \
-        expat \
-        git \
-        libffi \
-        mpdecimal \
-        ncurses-libs \
-        openssl \
-        parallel \
-        readline \
-        sqlite-libs \
-        tk \
-        xz \
-        zlib \
-    ;
-
-RUN set -eux; \
-    curl -L https://github.com/pyenv/pyenv-installer/raw/master/bin/pyenv-installer | bash; \
-    pyenv update
-
-FROM base AS builder
-
-# runtime dependencies
-RUN set -eux; \
-    apk update; \
-    apk add --no-cache \
-        bzip2-dev \
-        libffi-dev \
-        ncurses-dev \
-        openssl-dev \
-        readline-dev \
-        sqlite-dev \
-        tk-dev \
-        xz-dev \
-        zlib-dev \
-    ;
-
-FROM builder AS build-2.7.18
-RUN set -eux; pyenv install 2.7.18; \
-  find ${PYENV_ROOT}/versions -depth \
-        \( \
-            \( -type d -a \( -name test -o -name tests -o -name idle_test \) \) \
-            -o \( -type f -a -name 'wininst-*.exe' \) \
-        \) -exec rm -rf '{}' +
-
-FROM builder AS build-3.6.15
-RUN set -eux; pyenv install 3.6.15; \
-  find ${PYENV_ROOT}/versions -depth \
-        \( \
-            \( -type d -a \( -name test -o -name tests -o -name idle_test \) \) \
-            -o \( -type f -a -name 'wininst-*.exe' \) \
-        \) -exec rm -rf '{}' +
-
-FROM builder AS build-3.7.16
-RUN set -eux; pyenv install 3.7.16; \
-  find ${PYENV_ROOT}/versions -depth \
-        \( \
-            \( -type d -a \( -name test -o -name tests -o -name idle_test \) \) \
-            -o \( -type f -a -name 'wininst-*.exe' \) \
-        \) -exec rm -rf '{}' +
-
-FROM builder AS build-3.8.16
-RUN set -eux; pyenv install 3.8.16; \
-  find ${PYENV_ROOT}/versions -depth \
-        \( \
-            \( -type d -a \( -name test -o -name tests -o -name idle_test \) \) \
-            -o \( -type f -a -name 'wininst-*.exe' \) \
-        \) -exec rm -rf '{}' +
-
-FROM builder AS build-3.9.16
-RUN set -eux; pyenv install 3.9.16; \
-  find ${PYENV_ROOT}/versions -depth \
-        \( \
-            \( -type d -a \( -name test -o -name tests -o -name idle_test \) \) \
-            -o \( -type f -a -name 'wininst-*.exe' \) \
-        \) -exec rm -rf '{}' +
-
-FROM builder AS build-3.10.10
-RUN set -eux; pyenv install 3.10.10; \
-  find ${PYENV_ROOT}/versions -depth \
-        \( \
-            \( -type d -a \( -name test -o -name tests -o -name idle_test \) \) \
-            -o \( -type f -a -name 'wininst-*.exe' \) \
-        \) -exec rm -rf '{}' +
-
-FROM builder AS build-3.11.2
-RUN set -eux; pyenv install 3.11.2; \
-  find ${PYENV_ROOT}/versions -depth \
-        \( \
-            \( -type d -a \( -name test -o -name tests -o -name idle_test \) \) \
-            -o \( -type f -a -name 'wininst-*.exe' \) \
-        \) -exec rm -rf '{}' +
-
-FROM base AS tester
-COPY --from=build-2.7.18 /opt/pyenv/versions/2.7.18 /opt/pyenv/versions/2.7.18
-COPY --from=build-3.6.15 /opt/pyenv/versions/3.6.15 /opt/pyenv/versions/3.6.15
-COPY --from=build-3.7.16 /opt/pyenv/versions/3.7.16 /opt/pyenv/versions/3.7.16
-COPY --from=build-3.8.16 /opt/pyenv/versions/3.8.16 /opt/pyenv/versions/3.8.16
-COPY --from=build-3.9.16 /opt/pyenv/versions/3.9.16 /opt/pyenv/versions/3.9.16
-COPY --from=build-3.10.10 /opt/pyenv/versions/3.10.10 /opt/pyenv/versions/3.10.10
-COPY --from=build-3.11.2 /opt/pyenv/versions/3.11.2 /opt/pyenv/versions/3.11.2
-
-RUN set -eux; \
-    pyenv rehash; \
-    pyenv versions
-
-WORKDIR /intervaltree
-COPY . .
-CMD [ "scripts/testall.sh" ]
-
diff --git a/README.md b/README.md
index b7e24ae..ad8a685 100644
--- a/README.md
+++ b/README.md
@@ -364,7 +364,7 @@ Licensed under the [Apache License, version 2.0][Apache].
 The source code for this project is at https://github.com/chaimleib/intervaltree
 
 
-[build status badge]: https://github.com/chaimleib/intervaltree/workflows/ci/badge.svg
+[build status badge]: https://github.com/chaimleib/intervaltree/workflows/build/badge.svg
 [build status]: https://github.com/chaimleib/intervaltree/actions
 [GH]: https://github.com/chaimleib/intervaltree
 [issue tracker]: https://github.com/chaimleib/intervaltree/issues
diff --git a/pyproject.toml b/pyproject.toml
new file mode 100644
index 0000000..95e2454
--- /dev/null
+++ b/pyproject.toml
@@ -0,0 +1,44 @@
+[project]
+name = "intervaltree"
+description='Editable interval tree data structure'
+version = "3.2.0"
+authors = [
+  { name="Chaim Leib Halbert", email="chaim.leib.halbert@gmail.com" },
+]
+readme = "README.md"
+requires-python = ">=3.7"
+dependencies = [
+	"sortedcontainers < 3",
+]
+classifiers = [
+        'Development Status :: 5 - Production/Stable',
+        'Programming Language :: Python :: Implementation :: PyPy',
+        'Intended Audience :: Developers',
+        'Intended Audience :: Information Technology',
+        'Intended Audience :: Science/Research',
+        'Programming Language :: Python',
+        'Programming Language :: Python :: 3',
+        'Programming Language :: Python :: 3.7',
+        'Programming Language :: Python :: 3.8',
+        'Programming Language :: Python :: 3.9',
+        'Programming Language :: Python :: 3.10',
+        'Programming Language :: Python :: 3.11',
+        'Programming Language :: Python :: 3.12',
+        'Programming Language :: Python :: 3.13',
+        'License :: OSI Approved :: Apache Software License',
+        'Topic :: Scientific/Engineering :: Artificial Intelligence',
+        'Topic :: Scientific/Engineering :: Bio-Informatics',
+        'Topic :: Scientific/Engineering :: Information Analysis',
+        'Topic :: Software Development :: Libraries',
+        'Topic :: Text Processing :: General',
+        'Topic :: Text Processing :: Linguistic',
+        'Topic :: Text Processing :: Markup',
+]
+
+[project.urls]
+Homepage = "https://github.com/chaimleib/intervaltree"
+Issues = "https://github.com/chaimleib/intervaltree/issues"
+
+[build-system]
+requires = ["setuptools >= 61.0"]
+build-backend = "setuptools.build_meta"
diff --git a/scripts/testall.sh b/scripts/testall.sh
deleted file mode 100755
index 1364729..0000000
--- a/scripts/testall.sh
+++ /dev/null
@@ -1,15 +0,0 @@
-#!/bin/bash
-# Tests using `python setup.py test` using different versions of python.
-
-this_dir="$(dirname "$0")"
-export base_dir="$(dirname "$this_dir")"
-
-set -x
-code=0
-for ver in $(pyenv versions --bare | sort -V); do
-  pyenv global "$ver"
-  python --version
-  python "$base_dir/setup.py" test || code=1
-done
-set +x
-exit "$code"

From 2dc2de2689c5e7d1378b38d19272359506e74f67 Mon Sep 17 00:00:00 2001
From: Chaim Halbert <chaim.leib.halbert@gmail.com>
Date: Tue, 11 Mar 2025 14:37:59 -0700
Subject: [PATCH 02/17] fix(test): disable standalone test/intervals.py,
 optimality_test imports intervaltree

---
 test/intervals.py                  | 4 ++--
 test/optimality/optimality_test.py | 4 +++-
 2 files changed, 5 insertions(+), 3 deletions(-)

diff --git a/test/intervals.py b/test/intervals.py
index 7c2612e..1be24cb 100644
--- a/test/intervals.py
+++ b/test/intervals.py
@@ -126,10 +126,10 @@ def trepr(s):
         pprint(data, f)
 
 
-if __name__ == '__main__':
+# if __name__ == '__main__':
 #     ivs = gaps_rand()
 #     write_ivs_data('ivs3', ivs, docstring="""
 # Random integer ranges, with gaps.
 # """
 #     )
-    pprint(ivs)
+    # pprint(ivs)
diff --git a/test/optimality/optimality_test.py b/test/optimality/optimality_test.py
index eb2223d..a9faacf 100644
--- a/test/optimality/optimality_test.py
+++ b/test/optimality/optimality_test.py
@@ -25,8 +25,10 @@
 from test.optimality.optimality_test_matrix import OptimalityTestMatrix
 from test import data
 
+from intervaltree import IntervalTree
 
-matrix = OptimalityTestMatrix(verbose=1)
+
+matrix = OptimalityTestMatrix(verbose=True)
 matrix.run()
 
 

From e8cf497028a32bf54bf1a3558276d0b8dda4034e Mon Sep 17 00:00:00 2001
From: Chaim Halbert <chaim.leib.halbert@gmail.com>
Date: Tue, 11 Mar 2025 14:41:56 -0700
Subject: [PATCH 03/17] feat(ci): test in Python 2.7, 3.6+

---
 .github/workflows/build.yml | 2 +-
 1 file changed, 1 insertion(+), 1 deletion(-)

diff --git a/.github/workflows/build.yml b/.github/workflows/build.yml
index 7ddb206..e4670de 100644
--- a/.github/workflows/build.yml
+++ b/.github/workflows/build.yml
@@ -18,7 +18,7 @@ jobs:
     runs-on: ubuntu-latest
     strategy:
       matrix:
-        python-version: ["3.9", "3.10", "3.11", "3.12", "3.13"]
+        python-version: ["2.7", "3.6", "3.7", "3.8", "3.9", "3.10", "3.11", "3.12", "3.13"]
 
     steps:
     - uses: actions/checkout@v4

From 30a1b41a85d5e6c4e6a216eb03cea9e524bc9bd7 Mon Sep 17 00:00:00 2001
From: Chaim Halbert <chaim.leib.halbert@gmail.com>
Date: Tue, 11 Mar 2025 15:17:38 -0700
Subject: [PATCH 04/17] fix(ci): where python is too old for ubuntu-latest, use
 earlier ubuntu

---
 .github/workflows/build.yml | 23 +++++++++++++++++++----
 1 file changed, 19 insertions(+), 4 deletions(-)

diff --git a/.github/workflows/build.yml b/.github/workflows/build.yml
index e4670de..5c232d8 100644
--- a/.github/workflows/build.yml
+++ b/.github/workflows/build.yml
@@ -14,12 +14,27 @@ permissions:
 
 jobs:
   build:
-
-    runs-on: ubuntu-latest
     strategy:
       matrix:
-        python-version: ["2.7", "3.6", "3.7", "3.8", "3.9", "3.10", "3.11", "3.12", "3.13"]
-
+        python-version: ["3.6", "3.7", "3.8", "3.9", "3.10", "3.11", "3.12", "3.13"]
+        include:
+          - python-version: "3.6"
+            os: ubuntu-20.04
+          - python-version: "3.7"
+            os: ubuntu-22.04
+          - python-version: "3.8"
+            os: ubuntu-24.04
+          - python-version: "3.9"
+            os: ubuntu-24.04
+          - python-version: "3.10"
+            os: ubuntu-24.04
+          - python-version: "3.11"
+            os: ubuntu-24.04
+          - python-version: "3.12"
+            os: ubuntu-24.04
+          - python-version: "3.13"
+            os: ubuntu-24.04
+    runs-on: ${{ matrix.os }}
     steps:
     - uses: actions/checkout@v4
     - name: Set up Python ${{ matrix.python-version }}

From d3fb6beb1f2b0ec514d5c646a4c563625dc0a5fd Mon Sep 17 00:00:00 2001
From: Chaim Halbert <chaim.leib.halbert@gmail.com>
Date: Tue, 11 Mar 2025 21:30:50 -0700
Subject: [PATCH 05/17] feat(ci): split flake8 from pytest

---
 .github/workflows/flake8.yml                | 36 +++++++++++++++++++++
 .github/workflows/{build.yml => pytest.yml} | 14 +++-----
 2 files changed, 40 insertions(+), 10 deletions(-)
 create mode 100644 .github/workflows/flake8.yml
 rename .github/workflows/{build.yml => pytest.yml} (71%)

diff --git a/.github/workflows/flake8.yml b/.github/workflows/flake8.yml
new file mode 100644
index 0000000..1245e43
--- /dev/null
+++ b/.github/workflows/flake8.yml
@@ -0,0 +1,36 @@
+# This workflow will install Python dependencies, and lint with a single version of Python
+# For more information see: https://docs.github.com/en/actions/automating-builds-and-tests/building-and-testing-python
+
+name: flake8
+
+on:
+  push:
+    branches: [ "master", "gha" ]
+  pull_request:
+    branches: [ "master" ]
+
+permissions:
+  contents: read
+
+jobs:
+  flake8:
+    runs-on: ubuntu-latest
+    steps:
+    - uses: actions/checkout@v4
+    - name: Set up Python 3.13
+      uses: actions/setup-python@v5
+      with:
+        python-version: 3.13
+    - name: Display Python verison
+      run: python -c "import sys; print(sys.version)"
+    - name: Install dependencies
+      run: |
+        python -m pip install --upgrade pip
+        pip install flake8
+    - name: Lint with flake8
+      run: |
+        # stop the build if there are Python syntax errors or undefined names
+        flake8 . --count --select=E9,F63,F7,F82 --show-source --statistics
+        # exit-zero treats all errors as warnings. The GitHub editor is 127 chars wide
+        flake8 . --count --exit-zero --max-complexity=10 --max-line-length=127 --statistics
+
diff --git a/.github/workflows/build.yml b/.github/workflows/pytest.yml
similarity index 71%
rename from .github/workflows/build.yml
rename to .github/workflows/pytest.yml
index 5c232d8..066aa5c 100644
--- a/.github/workflows/build.yml
+++ b/.github/workflows/pytest.yml
@@ -1,7 +1,7 @@
-# This workflow will install Python dependencies, run tests and lint with a single version of Python
+# This workflow will install Python dependencies, and run tests supported versions of Python.
 # For more information see: https://docs.github.com/en/actions/automating-builds-and-tests/building-and-testing-python
 
-name: build
+name: pytest
 
 on:
   push:
@@ -13,7 +13,7 @@ permissions:
   contents: read
 
 jobs:
-  build:
+  pytest:
     strategy:
       matrix:
         python-version: ["3.6", "3.7", "3.8", "3.9", "3.10", "3.11", "3.12", "3.13"]
@@ -46,14 +46,8 @@ jobs:
     - name: Install dependencies
       run: |
         python -m pip install --upgrade pip
-        pip install flake8 pytest pytest-cov sortedcontainers
+        pip install pytest pytest-cov sortedcontainers
         if [ -f requirements.txt ]; then pip install -r requirements.txt; fi
-    - name: Lint with flake8
-      run: |
-        # stop the build if there are Python syntax errors or undefined names
-        flake8 . --count --select=E9,F63,F7,F82 --show-source --statistics
-        # exit-zero treats all errors as warnings. The GitHub editor is 127 chars wide
-        flake8 . --count --exit-zero --max-complexity=10 --max-line-length=127 --statistics
     - name: Test with pytest
       run: |
         pytest

From 6f347e963081efbb234f559f450d4d33a0b67642 Mon Sep 17 00:00:00 2001
From: Chaim Halbert <chaim.leib.halbert@gmail.com>
Date: Tue, 11 Mar 2025 21:37:44 -0700
Subject: [PATCH 06/17] refactor(ci): combine flake8 and pytest as 2 jobs of
 single workflow

---
 .github/workflows/flake8.yml                | 36 ---------------------
 .github/workflows/{pytest.yml => tests.yml} | 26 +++++++++++++--
 2 files changed, 24 insertions(+), 38 deletions(-)
 delete mode 100644 .github/workflows/flake8.yml
 rename .github/workflows/{pytest.yml => tests.yml} (62%)

diff --git a/.github/workflows/flake8.yml b/.github/workflows/flake8.yml
deleted file mode 100644
index 1245e43..0000000
--- a/.github/workflows/flake8.yml
+++ /dev/null
@@ -1,36 +0,0 @@
-# This workflow will install Python dependencies, and lint with a single version of Python
-# For more information see: https://docs.github.com/en/actions/automating-builds-and-tests/building-and-testing-python
-
-name: flake8
-
-on:
-  push:
-    branches: [ "master", "gha" ]
-  pull_request:
-    branches: [ "master" ]
-
-permissions:
-  contents: read
-
-jobs:
-  flake8:
-    runs-on: ubuntu-latest
-    steps:
-    - uses: actions/checkout@v4
-    - name: Set up Python 3.13
-      uses: actions/setup-python@v5
-      with:
-        python-version: 3.13
-    - name: Display Python verison
-      run: python -c "import sys; print(sys.version)"
-    - name: Install dependencies
-      run: |
-        python -m pip install --upgrade pip
-        pip install flake8
-    - name: Lint with flake8
-      run: |
-        # stop the build if there are Python syntax errors or undefined names
-        flake8 . --count --select=E9,F63,F7,F82 --show-source --statistics
-        # exit-zero treats all errors as warnings. The GitHub editor is 127 chars wide
-        flake8 . --count --exit-zero --max-complexity=10 --max-line-length=127 --statistics
-
diff --git a/.github/workflows/pytest.yml b/.github/workflows/tests.yml
similarity index 62%
rename from .github/workflows/pytest.yml
rename to .github/workflows/tests.yml
index 066aa5c..dfdabe2 100644
--- a/.github/workflows/pytest.yml
+++ b/.github/workflows/tests.yml
@@ -1,7 +1,7 @@
-# This workflow will install Python dependencies, and run tests supported versions of Python.
+# This workflow will install Python dependencies, lint, and run tests in supported versions of Python.
 # For more information see: https://docs.github.com/en/actions/automating-builds-and-tests/building-and-testing-python
 
-name: pytest
+name: tests
 
 on:
   push:
@@ -13,6 +13,7 @@ permissions:
   contents: read
 
 jobs:
+
   pytest:
     strategy:
       matrix:
@@ -52,3 +53,24 @@ jobs:
       run: |
         pytest
 
+  flake8:
+    runs-on: ubuntu-latest
+    steps:
+    - uses: actions/checkout@v4
+    - name: Set up Python 3.13
+      uses: actions/setup-python@v5
+      with:
+        python-version: 3.13
+    - name: Display Python verison
+      run: python -c "import sys; print(sys.version)"
+    - name: Install dependencies
+      run: |
+        python -m pip install --upgrade pip
+        pip install flake8
+    - name: Lint with flake8
+      run: |
+        # stop the build if there are Python syntax errors or undefined names
+        flake8 . --count --select=E9,F63,F7,F82 --show-source --statistics
+        # exit-zero treats all errors as warnings. The GitHub editor is 127 chars wide
+        flake8 . --count --exit-zero --max-complexity=10 --max-line-length=127 --statistics
+

From 55b067af41aba766cad439030381922474fa68d2 Mon Sep 17 00:00:00 2001
From: Chaim Halbert <chaim.leib.halbert@gmail.com>
Date: Tue, 11 Mar 2025 21:45:17 -0700
Subject: [PATCH 07/17] build: use requirements.txt files

---
 .github/workflows/tests.yml | 5 ++---
 requirements.txt            | 1 +
 requirements/common.txt     | 1 +
 requirements/flake8.txt     | 1 +
 requirements/pytest.txt     | 3 +++
 5 files changed, 8 insertions(+), 3 deletions(-)
 create mode 100644 requirements.txt
 create mode 100644 requirements/common.txt
 create mode 100644 requirements/flake8.txt
 create mode 100644 requirements/pytest.txt

diff --git a/.github/workflows/tests.yml b/.github/workflows/tests.yml
index dfdabe2..1c5503c 100644
--- a/.github/workflows/tests.yml
+++ b/.github/workflows/tests.yml
@@ -47,8 +47,7 @@ jobs:
     - name: Install dependencies
       run: |
         python -m pip install --upgrade pip
-        pip install pytest pytest-cov sortedcontainers
-        if [ -f requirements.txt ]; then pip install -r requirements.txt; fi
+        pip install -r requirements/pytest.txt
     - name: Test with pytest
       run: |
         pytest
@@ -66,7 +65,7 @@ jobs:
     - name: Install dependencies
       run: |
         python -m pip install --upgrade pip
-        pip install flake8
+        pip install -r requirements/flake8.txt
     - name: Lint with flake8
       run: |
         # stop the build if there are Python syntax errors or undefined names
diff --git a/requirements.txt b/requirements.txt
new file mode 100644
index 0000000..c58f7cb
--- /dev/null
+++ b/requirements.txt
@@ -0,0 +1 @@
+-r requirements/common.txt
diff --git a/requirements/common.txt b/requirements/common.txt
new file mode 100644
index 0000000..1e73a3a
--- /dev/null
+++ b/requirements/common.txt
@@ -0,0 +1 @@
+sortedcontainers==2.4.0
diff --git a/requirements/flake8.txt b/requirements/flake8.txt
new file mode 100644
index 0000000..3930480
--- /dev/null
+++ b/requirements/flake8.txt
@@ -0,0 +1 @@
+flake8
diff --git a/requirements/pytest.txt b/requirements/pytest.txt
new file mode 100644
index 0000000..5c843eb
--- /dev/null
+++ b/requirements/pytest.txt
@@ -0,0 +1,3 @@
+-r common.txt
+pytest
+pytest-cov

From e5aa4036baeb44d04392a995b527513db8f3c9f2 Mon Sep 17 00:00:00 2001
From: Chaim Halbert <chaim.leib.halbert@gmail.com>
Date: Tue, 11 Mar 2025 21:53:13 -0700
Subject: [PATCH 08/17] build: MANIFEST.in includes requirements dir

---
 MANIFEST.in | 2 +-
 1 file changed, 1 insertion(+), 1 deletion(-)

diff --git a/MANIFEST.in b/MANIFEST.in
index 260c74a..40d2b19 100644
--- a/MANIFEST.in
+++ b/MANIFEST.in
@@ -1,2 +1,2 @@
 include README.md CHANGELOG.md LICENSE.txt
-recursive-include test *
+recursive-include test requirements

From 0b3bcca4e9c8f76c6d6fabd9a0f95ba046e80ca3 Mon Sep 17 00:00:00 2001
From: Chaim Halbert <chaim.leib.halbert@gmail.com>
Date: Tue, 11 Mar 2025 21:54:10 -0700
Subject: [PATCH 09/17] build: pyproject.toml allows Python 3.6; remove deps
 from toml, use requirements.txt

---
 pyproject.toml | 6 ++----
 1 file changed, 2 insertions(+), 4 deletions(-)

diff --git a/pyproject.toml b/pyproject.toml
index 95e2454..9d9bd4d 100644
--- a/pyproject.toml
+++ b/pyproject.toml
@@ -6,10 +6,7 @@ authors = [
   { name="Chaim Leib Halbert", email="chaim.leib.halbert@gmail.com" },
 ]
 readme = "README.md"
-requires-python = ">=3.7"
-dependencies = [
-	"sortedcontainers < 3",
-]
+requires-python = ">=3.6"
 classifiers = [
         'Development Status :: 5 - Production/Stable',
         'Programming Language :: Python :: Implementation :: PyPy',
@@ -18,6 +15,7 @@ classifiers = [
         'Intended Audience :: Science/Research',
         'Programming Language :: Python',
         'Programming Language :: Python :: 3',
+        'Programming Language :: Python :: 3.6',
         'Programming Language :: Python :: 3.7',
         'Programming Language :: Python :: 3.8',
         'Programming Language :: Python :: 3.9',

From dbb3f13863a98c4ead89d7a5c9bc15eee7e8253a Mon Sep 17 00:00:00 2001
From: Chaim Halbert <chaim.leib.halbert@gmail.com>
Date: Tue, 11 Mar 2025 22:02:38 -0700
Subject: [PATCH 10/17] feat(ci): show test coverage

---
 .github/workflows/tests.yml | 3 ++-
 1 file changed, 2 insertions(+), 1 deletion(-)

diff --git a/.github/workflows/tests.yml b/.github/workflows/tests.yml
index 1c5503c..c12f5cc 100644
--- a/.github/workflows/tests.yml
+++ b/.github/workflows/tests.yml
@@ -50,7 +50,8 @@ jobs:
         pip install -r requirements/pytest.txt
     - name: Test with pytest
       run: |
-        pytest
+        coverage run -m pytest
+        coverage report
 
   flake8:
     runs-on: ubuntu-latest

From 22c00344251da49c2c4cc797f346380ed7c2c964 Mon Sep 17 00:00:00 2001
From: Chaim Halbert <chaim.leib.halbert@gmail.com>
Date: Tue, 11 Mar 2025 22:20:22 -0700
Subject: [PATCH 11/17] feat(ci): test on python 2.7

---
 .github/workflows/tests.yml | 18 +++++++++++++++++-
 pyproject.toml              |  2 ++
 2 files changed, 19 insertions(+), 1 deletion(-)

diff --git a/.github/workflows/tests.yml b/.github/workflows/tests.yml
index c12f5cc..d09ec01 100644
--- a/.github/workflows/tests.yml
+++ b/.github/workflows/tests.yml
@@ -51,7 +51,23 @@ jobs:
     - name: Test with pytest
       run: |
         coverage run -m pytest
-        coverage report
+        coverage report -m
+
+  pytest-python27:
+    runs-on: ubuntu-latest
+    container: coatldev/six:latest
+    steps:
+    - uses: actions/checkout@v4
+    - name: Display Python verison
+      run: python2 -c "import sys; print(sys.version)"
+    - name: Install dependencies
+      run: |
+        python2 -m pip install --upgrade pip
+        pip2 install -r requirements/pytest.txt
+    - name: Test with pytest
+      run: |
+        coverage2 run -m pytest
+        coverage2 report -m
 
   flake8:
     runs-on: ubuntu-latest
diff --git a/pyproject.toml b/pyproject.toml
index 9d9bd4d..3c6c1d0 100644
--- a/pyproject.toml
+++ b/pyproject.toml
@@ -14,6 +14,8 @@ classifiers = [
         'Intended Audience :: Information Technology',
         'Intended Audience :: Science/Research',
         'Programming Language :: Python',
+        'Programming Language :: Python :: 2',
+        'Programming Language :: Python :: 2.7',
         'Programming Language :: Python :: 3',
         'Programming Language :: Python :: 3.6',
         'Programming Language :: Python :: 3.7',

From 353b192027f5fcd5350247d38553dcf65b905215 Mon Sep 17 00:00:00 2001
From: Chaim Halbert <chaim.leib.halbert@gmail.com>
Date: Tue, 11 Mar 2025 22:30:54 -0700
Subject: [PATCH 12/17] feat(ci): test on Python 3.14

---
 .github/workflows/tests.yml | 4 +++-
 pyproject.toml              | 1 +
 2 files changed, 4 insertions(+), 1 deletion(-)

diff --git a/.github/workflows/tests.yml b/.github/workflows/tests.yml
index d09ec01..9dbab33 100644
--- a/.github/workflows/tests.yml
+++ b/.github/workflows/tests.yml
@@ -17,7 +17,7 @@ jobs:
   pytest:
     strategy:
       matrix:
-        python-version: ["3.6", "3.7", "3.8", "3.9", "3.10", "3.11", "3.12", "3.13"]
+        python-version: ["3.6", "3.7", "3.8", "3.9", "3.10", "3.11", "3.12", "3.13", "3.14.0-alpha.5"]
         include:
           - python-version: "3.6"
             os: ubuntu-20.04
@@ -35,6 +35,8 @@ jobs:
             os: ubuntu-24.04
           - python-version: "3.13"
             os: ubuntu-24.04
+          - python-version: "3.14.0-alpha.5"
+            os: ubuntu-24.04
     runs-on: ${{ matrix.os }}
     steps:
     - uses: actions/checkout@v4
diff --git a/pyproject.toml b/pyproject.toml
index 3c6c1d0..b586c7c 100644
--- a/pyproject.toml
+++ b/pyproject.toml
@@ -25,6 +25,7 @@ classifiers = [
         'Programming Language :: Python :: 3.11',
         'Programming Language :: Python :: 3.12',
         'Programming Language :: Python :: 3.13',
+        'Programming Language :: Python :: 3.14',
         'License :: OSI Approved :: Apache Software License',
         'Topic :: Scientific/Engineering :: Artificial Intelligence',
         'Topic :: Scientific/Engineering :: Bio-Informatics',

From e360dfd061cb2bf5477ab9dd93cb6611058787f1 Mon Sep 17 00:00:00 2001
From: Chaim Halbert <chaim.leib.halbert@gmail.com>
Date: Tue, 11 Mar 2025 22:42:05 -0700
Subject: [PATCH 13/17] feat(ci): test on Python 3.5

---
 .github/workflows/tests.yml | 10 +++++++---
 README.md                   |  2 +-
 pyproject.toml              |  1 +
 3 files changed, 9 insertions(+), 4 deletions(-)

diff --git a/.github/workflows/tests.yml b/.github/workflows/tests.yml
index 9dbab33..fc7da39 100644
--- a/.github/workflows/tests.yml
+++ b/.github/workflows/tests.yml
@@ -17,8 +17,10 @@ jobs:
   pytest:
     strategy:
       matrix:
-        python-version: ["3.6", "3.7", "3.8", "3.9", "3.10", "3.11", "3.12", "3.13", "3.14.0-alpha.5"]
+        python-version: ["3.5", "3.6", "3.7", "3.8", "3.9", "3.10", "3.11", "3.12", "3.13", "3.14.0-alpha.5"]
         include:
+          - python-version: "3.5"
+            os: ubuntu-20.04
           - python-version: "3.6"
             os: ubuntu-20.04
           - python-version: "3.7"
@@ -44,7 +46,9 @@ jobs:
       uses: actions/setup-python@v5
       with:
         python-version: ${{ matrix.python-version }}
-    - name: Display Python verison
+      env:
+        PIP_TRUSTED_HOST: "pypi.python.org pypi.org files.pythonhosted.org"
+    - name: Display Python version
       run: python -c "import sys; print(sys.version)"
     - name: Install dependencies
       run: |
@@ -60,7 +64,7 @@ jobs:
     container: coatldev/six:latest
     steps:
     - uses: actions/checkout@v4
-    - name: Display Python verison
+    - name: Display Python version
       run: python2 -c "import sys; print(sys.version)"
     - name: Install dependencies
       run: |
diff --git a/README.md b/README.md
index ad8a685..856084e 100644
--- a/README.md
+++ b/README.md
@@ -26,7 +26,7 @@ pip install intervaltree
 Features
 --------
 
-* Supports Python 2.7 and Python 3.6+ (Tested under 2.7, and 3.6 thru 3.11)
+* Supports Python 2.7 and Python 3.5+ (Tested under 2.7, and 3.5 thru 3.14)
 * Initializing
     * blank `tree = IntervalTree()`
     * from an iterable of `Interval` objects (`tree = IntervalTree(intervals)`)
diff --git a/pyproject.toml b/pyproject.toml
index b586c7c..1aa7ee6 100644
--- a/pyproject.toml
+++ b/pyproject.toml
@@ -17,6 +17,7 @@ classifiers = [
         'Programming Language :: Python :: 2',
         'Programming Language :: Python :: 2.7',
         'Programming Language :: Python :: 3',
+        'Programming Language :: Python :: 3.5',
         'Programming Language :: Python :: 3.6',
         'Programming Language :: Python :: 3.7',
         'Programming Language :: Python :: 3.8',

From dacb875308b56ae897aaa71941e555c5a523ae51 Mon Sep 17 00:00:00 2001
From: Chaim Halbert <chaim.leib.halbert@gmail.com>
Date: Tue, 11 Mar 2025 23:00:03 -0700
Subject: [PATCH 14/17] doc(readme): copyright 2025

---
 README.md | 2 +-
 1 file changed, 1 insertion(+), 1 deletion(-)

diff --git a/README.md b/README.md
index 856084e..3be58d8 100644
--- a/README.md
+++ b/README.md
@@ -356,7 +356,7 @@ Based on
 Copyright
 ---------
 
-* [Chaim Leib Halbert][GH], 2013-2023
+* [Chaim Leib Halbert][GH], 2013-2025
 * Modifications, [Konstantin Tretyakov][Konstantin intervaltree], 2014
 
 Licensed under the [Apache License, version 2.0][Apache].

From 1dec7a9878ad1d60b53ae03c9b0b5ae14339b821 Mon Sep 17 00:00:00 2001
From: Chaim Halbert <chaim.leib.halbert@gmail.com>
Date: Tue, 11 Mar 2025 23:02:37 -0700
Subject: [PATCH 15/17] doc(ci): update build badge URL

---
 README.md | 2 +-
 1 file changed, 1 insertion(+), 1 deletion(-)

diff --git a/README.md b/README.md
index 3be58d8..985f9dc 100644
--- a/README.md
+++ b/README.md
@@ -364,7 +364,7 @@ Licensed under the [Apache License, version 2.0][Apache].
 The source code for this project is at https://github.com/chaimleib/intervaltree
 
 
-[build status badge]: https://github.com/chaimleib/intervaltree/workflows/build/badge.svg
+[build status badge]: https://github.com/chaimleib/intervaltree/workflows/tests/badge.svg
 [build status]: https://github.com/chaimleib/intervaltree/actions
 [GH]: https://github.com/chaimleib/intervaltree
 [issue tracker]: https://github.com/chaimleib/intervaltree/issues

From 9cc6b195bac88b8bc5c9cddbb56f534b0acf7a27 Mon Sep 17 00:00:00 2001
From: Chaim Halbert <chaim.leib.halbert@gmail.com>
Date: Tue, 11 Mar 2025 23:36:48 -0700
Subject: [PATCH 16/17] build: pyproject.toml requires-python ~=2.7 or ~= 3.5;
 restore author; restore description for Py2&3

---
 pyproject.toml | 5 +++--
 1 file changed, 3 insertions(+), 2 deletions(-)

diff --git a/pyproject.toml b/pyproject.toml
index 1aa7ee6..776a3e0 100644
--- a/pyproject.toml
+++ b/pyproject.toml
@@ -1,12 +1,13 @@
 [project]
 name = "intervaltree"
-description='Editable interval tree data structure'
+description='Editable interval tree data structure for Python 2 and 3'
 version = "3.2.0"
 authors = [
   { name="Chaim Leib Halbert", email="chaim.leib.halbert@gmail.com" },
+  { name="Konstantin Tretyakov" },
 ]
 readme = "README.md"
-requires-python = ">=3.6"
+requires-python = ">= 2.7.18, !=3.0.*, !=3.1.*, !=3.2.*, !=3.3.*, !=3.4.*"
 classifiers = [
         'Development Status :: 5 - Production/Stable',
         'Programming Language :: Python :: Implementation :: PyPy',

From 39069155eafa2311e050fcb5eb570cff08c8009d Mon Sep 17 00:00:00 2001
From: Chaim Halbert <chaim.leib.halbert@gmail.com>
Date: Tue, 11 Mar 2025 23:48:56 -0700
Subject: [PATCH 17/17] doc: pyproject.toml license and keywords

---
 pyproject.toml | 2 ++
 1 file changed, 2 insertions(+)

diff --git a/pyproject.toml b/pyproject.toml
index 776a3e0..db128d8 100644
--- a/pyproject.toml
+++ b/pyproject.toml
@@ -8,6 +8,8 @@ authors = [
 ]
 readme = "README.md"
 requires-python = ">= 2.7.18, !=3.0.*, !=3.1.*, !=3.2.*, !=3.3.*, !=3.4.*"
+license = "Apache-2.0"
+keywords = ['interval-tree', 'data-structure', 'intervals', 'tree']
 classifiers = [
         'Development Status :: 5 - Production/Stable',
         'Programming Language :: Python :: Implementation :: PyPy',