4.0.0 installation

.github/dependabot.yml

@@ -0,0 +1,10 @@
+version: 2
+updates:
+    - package-ecosystem: github-actions
+      directory: /
+      schedule:
+          interval: weekly
+      groups:
+          dependencies:
+              patterns:
+                  - "*"

.github/workflows/test_pytest.yml

@@ -2,101 +2,101 @@ name: tests_pytest
 on: [push, pull_request, workflow_dispatch]
 
 defaults:
-  run:
-    shell: bash -l {0}
+    run:
+        shell: bash -l {0}
 
 jobs:
-  check_versions_matches:
-    name: Check deeptools version matches galaxy tools
-    runs-on: ubuntu-latest
-    if: github.base_ref == 'master'
-    steps:
-    - uses: actions/checkout@v4
-    - name: Check path
-      run: find /home/runner/work/deepTools/deepTools -name "pyproject.toml"
-    - name: Get Version of Deeptools
-      run: echo "deeptools_version=$(grep "version" /home/runner/work/deepTools/deepTools/pyproject.toml | awk '{print substr($NF, 2, length($NF) - 2)}')" >> $GITHUB_ENV
-    - name: Get Version of Galaxy tools
-      run: echo "galaxy_deeptools_version=$(grep "token.*TOOL_VERSION" /home/runner/work/deepTools/deepTools/galaxy/wrapper/deepTools_macros.xml | awk -F '>|<' '{print $3}')" >> $GITHUB_ENV
-    - name: Versions
-      run: | 
-        echo deeptools version=${deeptools_version}
-        echo deeptools version in galaxy=${galaxy_deeptools_version}
-    - name: Fail PR if versions not matching
-      run: |
-        if [ -z $galaxy_deeptools_version ]; then
-          echo "galaxy_deeptools_version not defined change the github action"
-          exit 1
-        fi
-        if [ -z $deeptools_version ]; then
-          echo "deeptools_version not defined change the github action"
-          exit 1
-        fi
-        if [ "$galaxy_deeptools_version" != "$deeptools_version" ]; then
-          echo "versions do not match"
-          exit 1
-        fi
-  build-linux:
-    name: Test on Linux
-    runs-on: ubuntu-latest
-    strategy:
-      matrix:
-        python-version: ['3.9','3.10', '3.11', '3.12', '3.13']
-    steps:
-      - uses: actions/checkout@v4
-      - uses: actions/setup-python@v5
-        with:
-          python-version: ${{ matrix.python-version }}
-          cache: 'pip'
-      - name: Install Rust
-        uses: actions-rust-lang/setup-rust-toolchain@v1
-      - name: build deeptools
-        run: |
-          python -m venv venv
-          source venv/bin/activate
-          pip install maturin
-          maturin develop --release --extras actions
-      - name: test deeptools
-        run: |
-          source venv/bin/activate
-          pytest -v
-      - name: build wheel
-        run: |
-          source venv/bin/activate
-          python -m build
-      - name: test wheel
-        run: |
-          source venv/bin/activate
-          pip install dist/*whl
-  build-osx:
-    name: Test on OSX
-    runs-on: macOS-latest
-    strategy:
-      matrix:
-        python-version: ['3.9','3.10', '3.11', '3.12', '3.13']
-    steps:
-      - uses: actions/checkout@v4
-      - uses: actions/setup-python@v5
-        with:
-          python-version: ${{ matrix.python-version }}
-          cache: 'pip'
-      - name: Install Rust
-        uses: actions-rust-lang/setup-rust-toolchain@v1
-      - name: build deeptools
-        run: |
-          python -m venv venv
-          source venv/bin/activate
-          pip install maturin
-          maturin develop --release --extras actions
-      - name: test deeptools
-        run: |
-          source venv/bin/activate
-          pytest -v
-      - name: build wheel
-        run: |
-          source venv/bin/activate
-          python -m build
-      - name: test wheel
-        run: |
-          source venv/bin/activate
-          pip install dist/*whl
+    check_versions_matches:
+        name: Check deeptools version matches galaxy tools
+        runs-on: ubuntu-latest
+        if: github.base_ref == 'master'
+        steps:
+            - uses: actions/checkout@v7
+            - name: Check path
+              run: find /home/runner/work/deepTools/deepTools -name "pyproject.toml"
+            - name: Get Version of Deeptools
+              run: echo "deeptools_version=$(grep "version" /home/runner/work/deepTools/deepTools/pyproject.toml | awk '{print substr($NF, 2, length($NF) - 2)}')" >> $GITHUB_ENV
+            - name: Get Version of Galaxy tools
+              run: echo "galaxy_deeptools_version=$(grep "token.*TOOL_VERSION" /home/runner/work/deepTools/deepTools/galaxy/wrapper/deepTools_macros.xml | awk -F '>|<' '{print $3}')" >> $GITHUB_ENV
+            - name: Versions
+              run: |
+                  echo deeptools version=${deeptools_version}
+                  echo deeptools version in galaxy=${galaxy_deeptools_version}
+            - name: Fail PR if versions not matching
+              run: |
+                  if [ -z $galaxy_deeptools_version ]; then
+                    echo "galaxy_deeptools_version not defined change the github action"
+                    exit 1
+                  fi
+                  if [ -z $deeptools_version ]; then
+                    echo "deeptools_version not defined change the github action"
+                    exit 1
+                  fi
+                  if [ "$galaxy_deeptools_version" != "$deeptools_version" ]; then
+                    echo "versions do not match"
+                    exit 1
+                  fi
+    build-linux:
+        name: Test on Linux
+        runs-on: ubuntu-latest
+        strategy:
+            matrix:
+                python-version: ["3.12", "3.13", "3.14"]
+        steps:
+            - uses: actions/checkout@v7
+            - uses: actions/setup-python@v6
+              with:
+                  python-version: ${{ matrix.python-version }}
+                  cache: "pip"
+            - name: Install Rust
+              uses: actions-rust-lang/setup-rust-toolchain@v1
+            - name: build deeptools
+              run: |
+                  python -m venv venv
+                  source venv/bin/activate
+                  pip install maturin
+                  maturin develop --release --extras actions
+            - name: test deeptools
+              run: |
+                  source venv/bin/activate
+                  pytest -v
+            - name: build wheel
+              run: |
+                  source venv/bin/activate
+                  python -m build
+            - name: test wheel
+              run: |
+                  source venv/bin/activate
+                  pip install dist/*whl
+    build-osx:
+        name: Test on OSX
+        runs-on: macOS-latest
+        strategy:
+            matrix:
+                python-version: ["3.12", "3.13", "3.14"]
+        steps:
+            - uses: actions/checkout@v7
+            - uses: actions/setup-python@v6
+              with:
+                  python-version: ${{ matrix.python-version }}
+                  cache: "pip"
+            - name: Install Rust
+              uses: actions-rust-lang/setup-rust-toolchain@v1
+            - name: build deeptools
+              run: |
+                  python -m venv venv
+                  source venv/bin/activate
+                  pip install maturin
+                  maturin develop --release --extras actions
+            - name: test deeptools
+              run: |
+                  source venv/bin/activate
+                  pytest -v
+            - name: build wheel
+              run: |
+                  source venv/bin/activate
+                  python -m build
+            - name: test wheel
+              run: |
+                  source venv/bin/activate
+                  pip install dist/*whl

.github/workflows/test_rust.yml

@@ -1,14 +1,19 @@
 name: tests_rust
-on: [push, pull_request, workflow_dispatch]
+on:
+    push:
+    pull_request:
+    workflow_dispatch:
+    schedule:
+        - cron: "0 0 * * 0"
 
 jobs:
-  cargo_test:
-    name: run cargo test
-    runs-on: ubuntu-latest
-    steps:
-      - uses: actions/checkout@v4
-      - run: rustup update stable && rustup default stable
-      - name: cargo build
-        run: cargo build --verbose
-      - name: cargo test
-        run: cargo test --verbose
+    cargo_test:
+        name: run cargo test
+        runs-on: ubuntu-latest
+        steps:
+            - uses: actions/checkout@v7
+            - run: rustup update stable && rustup default stable
+            - name: cargo build
+              run: cargo build --verbose
+            - name: cargo test
+              run: cargo test --verbose

.gitignore

@@ -69,4 +69,7 @@ target*
 # jupyter notebooks
 .ipynb_checkpoints
 *.ipynb_checkpoints
-*.ipynb
+*.ipynb
+
+# pixi
+.pixi*

Cargo.toml

@@ -10,13 +10,13 @@ crate-type = ["cdylib"]
 
 [dependencies]
 openssl-sys = { version = "*", features = ["vendored"] }
-pyo3 = { version = "0.23.4", features = ["extension-module"] }
-rust-htslib = "0.49.0"
-rayon = "1.10.0"
-itertools = "0.14.0"
-bigtools = "0.5.3"
+pyo3 = { version = "*", features = ["extension-module"] }
+rust-htslib = "*"
+rayon = "*"
 tokio = "*"
+itertools = "*"
+bigtools = "*"
 flate2 = "*"
 tempfile = "*"
-ndarray = "0.16.1"
-ndarray-npy = "*"
+ndarray = "*"
+ndarray-npy = "*"