Merge branch 'master' into paper

.environment.yml

@@ -4,69 +4,113 @@ channels:
   - conda-forge
   - defaults
 dependencies:
-  - ca-certificates=2021.10.8
-  - certifi=2021.10.8
+  - ca-certificates>=2021.10.8
+  - certifi>=2021.10.8
   - ipykernel
-  - libcxx=12.0.0
+  - libcxx>=12.0.0
   - libffi>=3.3
-  - ncurses=6.3
+  - ncurses>=6.4
   - make=4.3
-  - openssl=1.1.1q
-  - pip=21.2.4
-  - python=3.9.13
-  - python_abi=3.9
-  - readline=8.1.2
-  - libzlib=1.2.13
+  - openssl>=1.1.1q
+  - pip>=21.2.4
+  - python=3.10.12
+  - python_abi=3.10
+  - readline>=8.1.2
+  - libzlib>=1.2.13
   - rust=1.67.1
   - setuptools=61.2.0
   - sqlite>=3.38.3
   - tk>=8.6.11
-  - tzdata=2022a
-  - wheel=0.37.1
-  - xz=5.2.5
+  - tzdata>=2022a
+  - wheel>=0.37.1
+  - xz>=5.2.5
   - zlib>=1.2.12
   - pip:
-      - alabaster==0.7.12
-      - babel==2.10.1
-      - charset-normalizer==2.0.12
-      - docutils==0.17.1
-      - idna==3.3
-      - imagesize==1.3.0
-      - importlib-metadata==4.11.3
-      - jupyter==1.0.0
-      - markdown-it-py==2.1.0
-      - markupsafe==2.1.1
+      - accessible-pygments==0.0.4
+      - alabaster==0.7.13
+      - appnope==0.1.3
+      - asttokens==2.2.1
+      - attrs==23.1.0
+      - autodocsumm==0.2.11
+      - Babel==2.12.1
+      - backcall==0.2.0
+      - beautifulsoup4==4.12.2
+      - bleach==6.0.0
+      - certifi==2023.5.7
+      - charset-normalizer==3.1.0
+      - contourpy==1.1.0
+      - cycler==0.11.0
+      - decorator==5.1.1
+      - defusedxml==0.7.1
+      - docutils==0.19
+      - executing==1.2.0
+      - fastjsonschema==2.17.1
+      - fonttools==4.40.0
+      - idna==3.4
+      - imagesize==1.4.1
+      - ipython==8.14.0
+      - jedi==0.18.2
+      - Jinja2==3.1.2
+      - jsonpickle==3.0.1
+      - jsonschema==4.17.3
+      - jupyter_client==8.3.0
+      - jupyter_core==5.3.1
+      - jupyterlab-pygments==0.2.2
+      - kiwisolver==1.4.4
+      - MarkupSafe==2.1.3
       - matplotlib==3.7.1
-      - maturin==0.14.17
-      - mdit-py-plugins==0.3.0
-      - mdurl==0.1.1
-      - myst-parser==0.17.2
+      - matplotlib-inline==0.1.6
+      - maturin==1.1.0
+      - mistune==3.0.1
+      - nbclient==0.8.0
+      - nbconvert==7.6.0
+      - nbformat==5.9.0
+      - nbsphinx==0.9.2
+      - networkx==3.1
+      - numpy==1.25.0
       - numpydoc==1.5.0
-      - packaging==21.3
-      - pandas==2.0.2
-      - patchelf==0.17.2.1
-      - poetry==1.2.0
-      - pygments==2.12.0
-      - pyparsing==3.0.8
-      - pytz==2022.1
-      - pyyaml==6.0
+      - packaging==23.1
+      - pandas==2.0.3
+      - pandocfilters==1.5.0
+      - parso==0.8.3
+      - pexpect==4.8.0
+      - pickleshare==0.7.5
+      - Pillow==10.0.0
+      - platformdirs==3.8.0
+      - prompt-toolkit==3.0.39
+      - ptyprocess==0.7.0
+      - pure-eval==0.2.2
       - pydata-sphinx-theme==0.13.3
+      - Pygments==2.15.1
+      - pyparsing==3.1.0
+      - pyrsistent==0.19.3
+      - python-dateutil==2.8.2
+      - pytz==2023.3
       - pyvis==0.3.2
-      - requests==2.27.1
+      - pyzmq==25.1.0
+      - requests==2.31.0
+      - six==1.16.0
       - snowballstemmer==2.2.0
-      - nbsphinx>=0.8.7
-      - sphinx==4.5.0
-      - sphinx-rtd-theme==1.0.0
-      - sphinxcontrib-applehelp==1.0.2
-      - sphinx_copybutton==0.5.2
+      - soupsieve==2.4.1
+      - Sphinx==6.2.1
+      - sphinx-copybutton==0.5.2
+      - sphinx-toggleprompt==0.4.0
       - sphinx_design==0.4.1
+      - sphinxcontrib-applehelp==1.0.4
       - sphinxcontrib-devhelp==1.0.2
-      - sphinxcontrib-htmlhelp==2.0.0
-      - sphinx_toggleprompt==0.4.0
-      - sphinx-tabs==3.4.0
+      - sphinxcontrib-htmlhelp==2.0.1
       - sphinxcontrib-jsmath==1.0.1
       - sphinxcontrib-qthelp==1.0.3
       - sphinxcontrib-serializinghtml==1.1.5
-      - typing-extensions==4.2.0
-      - urllib3==1.26.9
-      - zipp==3.8.0
+      - stack-data==0.6.2
+      - tinycss2==1.2.1
+      - tomli==2.0.1
+      - tornado==6.3.2
+      - traitlets==5.9.0
+      - typing_extensions==4.7.1
+      - tzdata==2023.3
+      - urllib3==2.0.3
+      - wcwidth==0.2.6
+      - webencodings==0.5.1
+
+

.fleet/settings.json

@@ -0,0 +1,3 @@
+{
+    "editor.guides": []
+}

.github/workflows/_release_python.yml

@@ -18,8 +18,7 @@ jobs:
     runs-on: ubuntu-latest
     strategy:
       matrix:
-        target: [x86_64, aarch64, armv7]
-        python: ['3.9', '3.10']
+        target: [x86_64, aarch64]
     steps:
       - name: "Check if user has write access"
         uses: "lannonbr/[email protected]"
@@ -43,16 +42,18 @@ jobs:
           ref: ${{ inputs.base }}
       - uses: actions/setup-python@v4
         with:
-          python-version: ${{ matrix.python }}
-      - name: Setup QEMU
-        uses: docker/setup-qemu-action@v1
+          python-version: |
+            3.8
+            3.9
+            3.10
+            3.11
       - name: Build wheels
         uses: PyO3/maturin-action@v1
         with:
           working-directory: ./python
           command: build
           target: ${{ matrix.target }}
-          args: --release --out dist --find-interpreter
+          args: --release --out dist -i python3.7 -i python3.8 -i python3.9 -i python3.10 -i python3.11
           manylinux: 2014
           before-script-linux: |
             if [[ -f /etc/os-release ]]; then
@@ -101,7 +102,6 @@ jobs:
     strategy:
       matrix:
         target: [x64]
-        python: ['3.9', '3.10']
     steps:
       - name: "Check if user has write access"
         uses: "lannonbr/[email protected]"
@@ -114,15 +114,19 @@ jobs:
           ref: ${{ inputs.base }}
       - uses: actions/setup-python@v4
         with:
-          python-version: ${{ matrix.python }}
+          python-version: |
+            3.8
+            3.9
+            3.10
+            3.11
           architecture: ${{ matrix.target }}
       - name: Build wheels
         uses: PyO3/maturin-action@v1
         with:
           working-directory: ./python
           command: build
           target: ${{ matrix.target }}
-          args: --release --out dist --find-interpreter
+          args: --release --out dist -i python3.7 -i python3.8 -i python3.9 -i python3.10 -i python3.11
       - name: Upload wheels to gh artifact
         uses: actions/upload-artifact@v3
         with:
@@ -133,7 +137,6 @@ jobs:
     strategy:
       matrix:
         target: [x86_64, aarch64]
-        python: ['3.9', '3.10']
     steps:
       - name: "Check if user has write access"
         uses: "lannonbr/[email protected]"
@@ -157,7 +160,11 @@ jobs:
           ref: ${{ inputs.base }}
       - uses: actions/setup-python@v4
         with:
-          python-version: ${{ matrix.python }}
+          python-version: |
+            3.8
+            3.9
+            3.10
+            3.11
       - name: Build wheels
         uses: PyO3/maturin-action@v1
         with:

.github/workflows/_release_rust.yml

@@ -61,27 +61,9 @@ jobs:
         with:
           command: publish
           args: --token ${{ secrets.CRATES_TOKEN }} --package raphtory --allow-dirty
-      - name: "Publish raphtory-io to crates.io"
-        if: ${{ !inputs.dry_run }}
-        uses: actions-rs/cargo@v1
-        with:
-          command: publish
-          args: --token ${{ secrets.CRATES_TOKEN }} --package raphtory-io --allow-dirty
       - name: "Publish raphtory-graphql to crates.io"
         if: ${{ !inputs.dry_run }}
         uses: actions-rs/cargo@v1
         with:
           command: publish
           args: --token ${{ secrets.CRATES_TOKEN }} --package raphtory-graphql --allow-dirty
-      - name: "Publish py-raphtory to crates.io"
-        if: ${{ !inputs.dry_run }}
-        uses: actions-rs/cargo@v1
-        with:
-          command: publish
-          args: --token ${{ secrets.CRATES_TOKEN }} --package py-raphtory --allow-dirty
-      - name: "Publish raphtory-pymodule to crates.io"
-        if: ${{ !inputs.dry_run }}
-        uses: actions-rs/cargo@v1
-        with:
-          command: publish
-          args: --token ${{ secrets.CRATES_TOKEN }} --package raphtory-pymodule --allow-dirty

.github/workflows/binder_auto_build.yml

@@ -11,6 +11,6 @@ jobs:
     steps:
       - uses: s-weigand/trigger-mybinder-build@v1
         with:
-          target-repo: raphtory/raphtory
+          target-repo: pometry/raphtory
           service-name: gh
           use-default-build-servers: true

.github/workflows/code_coverage.yml

@@ -51,7 +51,7 @@ jobs:
         with:
           command: clean
       - name: Run tests (rust)
-        run: cargo test -p raphtory
+        run: cargo test -p raphtory --features "io python"
         env:
           CARGO_INCREMENTAL: '0'
           RUSTFLAGS: '-Zprofile -Ccodegen-units=1 -Cinline-threshold=0 -Clink-dead-code -Coverflow-checks=off -Cpanic=abort -Zpanic_abort_tests'
@@ -66,7 +66,7 @@ jobs:
         name: Run rust tests (rust-grcov) and collect coverage
         uses: actions-rs/[email protected]
       - name: Run python tests and collect coverage
-        run: pytest --cov=./ --cov-report=xml
+        run: cd python/tests && pytest --cov=./ --cov-report=xml
       - name: Codecov
         uses: codecov/[email protected]
         with:

.github/workflows/rust_format_check.yml

@@ -0,0 +1,31 @@
+# this workflow checks out the code, and installs nightly build of cargo and runs a cargo +nightly fmt --all -- --check and fails workflow if any code is not formatted
+#
+
+name: Rust format check
+on:
+  workflow_call:
+    inputs:
+      fail_if_not_formatted:
+        type: boolean
+        default: true
+        required: false
+        description: "Fail the workflow if any code is not formatted"
+
+jobs:
+    rust-format-check:
+      runs-on: ubuntu-latest
+      steps:
+        - uses: actions/checkout@v2
+        - name: Setup Rust
+          uses: actions-rs/toolchain@v1
+          with:
+            toolchain: nightly
+            override: true
+            components: rustfmt
+        - name: Run rust format check
+          run: |
+            if [ ${{ inputs.fail_if_not_formatted }} == true ]; then
+                cargo +nightly fmt --all -- --check
+            else
+                cargo +nightly fmt --all -- --check || true
+            fi

.github/workflows/test.yml

@@ -3,23 +3,25 @@ on:
   push:
     branches:
       - master
-  pull_request:
-    branches:
-      - master
 
 concurrency:
   group: ${{ github.workflow }}-${{ github.event.pull_request.number || github.ref }}
   cancel-in-progress: true
 
 
 jobs:
+  rust-format-check:
+    name: Rust format check
+    uses: ./.github/workflows/rust_format_check.yml
   call-test-rust-workflow-in-local-repo:
     name: Run Rust tests
     uses: ./.github/workflows/test_rust_workflow.yml
     secrets: inherit
   call-test-python-workflow-in-local-repo:
     name: Run Python tests
     uses: ./.github/workflows/test_python_workflow.yml
+    with:
+      test_python_lower: true
     secrets: inherit
   call-benchmark-workflow-in-local-repo:
     name: Run benchmarks