From 2f966ce4de8185121126bff945737629b42d1329 Mon Sep 17 00:00:00 2001
From: Kaalleen <36401965+kaalleen@users.noreply.github.com>
Date: Sun, 15 Oct 2023 07:08:36 +0200
Subject: Update shapely (#2471)

* update shapely
* pin pyinstaller to 5.13.2 (issues with macOS) (rejbasket)
* macOS: do not install shapely from binary, but remove .dylibs folder (breaks notarizazion) (rejbasket)
---
 .github/workflows/build.yml     | 20 +++++++++-----------
 bin/build-distribution-archives | 18 ++++++++++++++++--
 lib/stitches/auto_fill.py       | 13 +++++--------
 lib/stitches/guided_fill.py     |  2 +-
 requirements.txt                |  3 ++-
 5 files changed, 33 insertions(+), 23 deletions(-)

diff --git a/.github/workflows/build.yml b/.github/workflows/build.yml
index 3a0a50b1..d7d46891 100644
--- a/.github/workflows/build.yml
+++ b/.github/workflows/build.yml
@@ -72,7 +72,7 @@ jobs:
           python -m pip install https://extras.wxpython.org/wxPython4/extras/linux/gtk3/ubuntu-20.04/wxPython-4.2.1-cp38-cp38-linux_x86_64.whl
 
           python -m pip install -r requirements.txt
-          python -m pip install pyinstaller
+          python -m pip install pyinstaller==5.13.2
 
           # scipy gives us a ELF error when stripped
           sudo apt-get install gcc g++ gfortran python3-dev libopenblas-dev liblapack-dev
@@ -116,8 +116,9 @@ jobs:
           # Numpy and Scipy version for older cpu compatibility
           python -m pip install numpy==1.23.1
           python -m pip install scipy==1.9.0
+          pip install wxPython
           python -m pip install -r requirements.txt
-          python -m pip install pyinstaller
+          python -m pip install pyinstaller==5.13.2
 
           echo "${{ env.pythonLocation }}\bin" >> $GITHUB_PATH
       - shell: bash
@@ -163,8 +164,9 @@ jobs:
           git config --system core.longpaths true
           python -m pip install --upgrade pip
           python -m pip install wheel
+          pip install wxPython
           python -m pip install -r requirements.txt
-          python -m pip install pyinstaller
+          python -m pip install pyinstaller==5.13.2
 
           echo "${{ env.pythonLocation }}\bin" >> $GITHUB_PATH
       - shell: bash
@@ -198,7 +200,7 @@ jobs:
           submodules: recursive
       - uses: actions/setup-python@v4
         with:
-          python-version: '3.8.x'
+          python-version: '3.9.x'
       - uses: actions/setup-node@v3
         with:
           node-version: '16.x'
@@ -207,7 +209,7 @@ jobs:
         run: |
           brew update
 
-          brew install gtk+3 pkg-config gobject-introspection geos libffi gettext || true
+          brew install gtk+3 pkg-config gobject-introspection geos libffi gettext jq gnu-getopt || true
 
           export LDFLAGS="-L/usr/local/opt/libffi/lib"
           export PKG_CONFIG_PATH="/usr/local/opt/libffi/lib/pkgconfig"
@@ -221,13 +223,9 @@ jobs:
           pip --version
           pip install wheel
           pip install PyGObject
-          pip install wxpython==4.1.1
+          pip install wxPython
           pip install -r requirements.txt
-          # with --no-binary argument may fix notary issues as well shapely speedups error issue
-          pip install -U lxml --no-binary lxml
-          pip uninstall --yes shapely
-          pip install -v -U Shapely==1.8.5 --no-binary Shapely
-          pip install pyinstaller
+          pip install pyinstaller==5.13.2
 
           echo "${{ env.pythonLocation }}/bin" >> $GITHUB_PATH
       - shell: bash
diff --git a/bin/build-distribution-archives b/bin/build-distribution-archives
index b44cad46..021461df 100644
--- a/bin/build-distribution-archives
+++ b/bin/build-distribution-archives
@@ -8,6 +8,8 @@ if [ "$BUILD" = "osx" ]; then
     # adding version to Info.plist
     plutil -replace CFBundleShortVersionString -string ${VERSION} dist/inkstitch.app/Contents/Info.plist
     rm -rf dist/inkstitch/
+    # this removes the extra dylibs that cause notary to fail.
+    rm -rf dist/inkstitch.app/Contents/MacOS/shapely/.dylibs
     # Install location for pkgbuild
     PKG_INSTALL_PATH="/tmp/inkstitch/"
     # Checking arch of macos and setting path of electron for arm64 or intel
@@ -70,11 +72,23 @@ if [ "$BUILD" = "osx" ]; then
                                                 --team-id '929A568N58' \
                                                 --password "${NOTARY_PASSWORD}"
             echo "Invoking notary process"
-            xcrun notarytool submit --wait \
+            xcrun notarytool submit -f json --wait \
                                     --keychain-profile "inkstitch-profile" \
-                                    artifacts/inkstitch-${VERSION}-${OS}.pkg
+                                    artifacts/inkstitch-${VERSION}-${OS}.pkg 2>&1 | tee /tmp/notarization_info.json
             echo "Stapling the pkg for release"
             xcrun stapler staple artifacts/inkstitch-${VERSION}-${OS}.pkg
+            echo "Fetching the Notary Log"
+            # code snippet is from https://github.com/ddev/signing_tools/blob/master/macos_notarize.sh
+            status=$(jq -r .status </tmp/notarization_info.json)
+            id=$(jq -r .id </tmp/notarization_info.json)
+            echo "status=${status} id=${id}"
+            xcrun notarytool log --apple-id "${NOTARY_ACCOUNT}" --team-id '929A568N58'  --password "${NOTARY_PASSWORD}" ${id} -f json >/tmp/notarization_log.json
+            issues=$(jq -r .issues </tmp/notarization_log.json)
+            if [ "$issues" != "null" ]; then
+                printf "There are issues with the notarization (${issues})\n"
+                printf "=== Log output === \n$(cat /tmp/notarization_log.json)\n"
+                exit 7;
+            fi;
         fi
     else
         # local builds will not be signed or notarized
diff --git a/lib/stitches/auto_fill.py b/lib/stitches/auto_fill.py
index 50eea18e..b4d63224 100644
--- a/lib/stitches/auto_fill.py
+++ b/lib/stitches/auto_fill.py
@@ -380,14 +380,11 @@ def process_travel_edges(graph, fill_stitch_graph, shape, travel_edges):
 
         edge = (p1.as_tuple(), p2.as_tuple(), 'travel')
 
-        for segment in strtree.query(ls):
-            # It seems like the STRTree only gives an approximate answer of
-            # segments that _might_ intersect ls.  Refining the result is
-            # necessary but the STRTree still saves us a ton of time.
-            if segment.crosses(ls):
-                start = segment.coords[0]
-                end = segment.coords[-1]
-                fill_stitch_graph[start][end]['segment']['underpath_edges'].append(edge)
+        for segment in strtree.query(ls, predicate='crosses'):
+            segment_geom = strtree.geometries.take(segment)
+            start = segment_geom.coords[0]
+            end = segment_geom.coords[-1]
+            fill_stitch_graph[start][end]['segment']['underpath_edges'].append(edge)
 
         # The weight of a travel edge is the length of the line segment.
         weight = p1.distance(p2)
diff --git a/lib/stitches/guided_fill.py b/lib/stitches/guided_fill.py
index e4793838..67ad4ccd 100644
--- a/lib/stitches/guided_fill.py
+++ b/lib/stitches/guided_fill.py
@@ -268,7 +268,7 @@ def intersect_region_with_grating_guideline(shape, line, row_spacing, num_stagge
         stitched_line = apply_stitches(offset_line, max_stitch_length, num_staggers, row_spacing, row)
         intersection = shape.intersection(stitched_line)
 
-        if shape_envelope.intersects(stitched_line):
+        if not intersection.is_empty and shape_envelope.intersects(stitched_line):
             for segment in take_only_line_strings(intersection).geoms:
                 rows.append(segment.coords[:])
             row += direction
diff --git a/requirements.txt b/requirements.txt
index 14d72270..5822c193 100644
--- a/requirements.txt
+++ b/requirements.txt
@@ -7,7 +7,7 @@ wxPython>=4.1.1
 
 backports.functools_lru_cache
 networkx
-shapely==1.8.5
+shapely
 lxml
 appdirs
 numpy
@@ -26,3 +26,4 @@ diskcache
 flask-cors
 pywinutils ; sys_platform == 'win32'
 pywin32 ; sys_platform == 'win32'
+
-- 
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