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#2407 - The ordering of branches of cascade reactions and reactions t…
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…hemselves should be the same on Load/Save from/to RDF (#2570)
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@even1024
even1024 authored Oct 24, 2024
1 parent 7b6a23c commit 6b97e43
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15 changes: 10 additions & 5 deletions .github/workflows/indigo-ci.yaml
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Expand Up @@ -29,7 +29,7 @@ jobs:
git fetch --tags -f
- name: Check
run: |
python3 -m pip install -r api/python/requirements_dev.txt
python3 -m pip install -r api/python/requirements_dev.txt --break-system-packages
.ci/static_analysis_check.sh
build_indigo_libs_x86_64:
Expand Down Expand Up @@ -208,7 +208,7 @@ jobs:
name: indigo-libs-macos-aarch64
path: dist/
- name: Install Python test dependencies
run: python3 -m pip install -r api/python/requirements_dev.txt
run: python3 -m pip install -r api/python/requirements_dev.txt --break-system-packages
- name: Build wrappers
run: |
mkdir build
Expand Down Expand Up @@ -364,7 +364,7 @@ jobs:
python-version: '3.9'
architecture: x86
- name: Install Pillow
run: python -m pip install Pillow
run: python -m pip install Pillow --break-system-packages
- name: Install wrappers Windows
if: ${{ startsWith(matrix.os, 'windows') }}
run: Get-ChildItem dist -Filter *win32*.whl -Recurse | % { python -m pip install $_.FullName --break-system-packages }
Expand Down Expand Up @@ -548,6 +548,11 @@ jobs:
run: |
curl -Lo dotnet.tar.gz https://download.visualstudio.microsoft.com/download/pr/270b615f-5281-4c58-980f-d9f7a08db642/3e874492a9cb0d5b87195c596b46d609/dotnet-sdk-6.0.421-osx-x64.tar.gz
mkdir -p ${{ github.workspace }}/tmp/dotnet && tar zxf dotnet.tar.gz -C ${{ github.workspace }}/tmp/dotnet
- name: Install dotnet 6 linux
if: ${{ startsWith(matrix.os, 'ubuntu') }}
run: |
sudo apt update
sudo apt install -y dotnet-host dotnet-sdk-6.0
- name: Prepare UNIX
if: ${{ !startsWith(matrix.os, 'windows') }}
run: |
Expand Down Expand Up @@ -1037,7 +1042,7 @@ jobs:
docker run --rm -d -p 5432:5432 -e "POSTGRES_PASSWORD=password" -v /home:/home epmlsop/bingo-postgres:${{ matrix.postgres_major_version }}-latest
- name: Install dev dependencies
run: |
pip install -r bingo/tests/requirements.txt
pip install -r bingo/tests/requirements.txt --break-system-packages
- name: Run Bingo tests
run: |
export PYTHONPATH=${{ github.workspace }}/bingo/bingo-elastic/python
Expand Down Expand Up @@ -1401,4 +1406,4 @@ jobs:
export clean_tag=${tag/refs\/tags\/indigo-/}
docker tag epmlsop/indigo-service:enhanced-latest epmlsop/indigo-service:enhanced-${clean_tag}
docker push epmlsop/indigo-service:enhanced-${clean_tag}
docker push epmlsop/indigo-service:enhanced-latest
docker push epmlsop/indigo-service:enhanced-latest
2 changes: 2 additions & 0 deletions api/tests/integration/ref/formats/ket_cdxml.py.out
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@@ -1,4 +1,6 @@
*** KET to CDXML to KET ***
2558-missed.cdxml:SUCCEED
2558-missed.ket:SUCCEED
961-text_size.cdxml:SUCCEED
961-text_size.ket:SUCCEED
agents.cdxml:SUCCEED
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1 change: 1 addition & 0 deletions api/tests/integration/ref/formats/ket_to_rdf.py.out
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Expand Up @@ -2,6 +2,7 @@
multi.rdf:SUCCEED
pathway1.rdf:SUCCEED
pathway10.rdf:SUCCEED
pathway11.rdf:SUCCEED
pathway2.rdf:SUCCEED
pathway3.rdf:SUCCEED
pathway4.rdf:SUCCEED
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1 change: 1 addition & 0 deletions api/tests/integration/ref/formats/rdf_to_cdxml.py.out
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@@ -1,6 +1,7 @@
*** RDF to CDXML ***
pathway1.cdxml:SUCCEED
pathway10.cdxml:SUCCEED
pathway11.cdxml:SUCCEED
pathway2.cdxml:SUCCEED
pathway3.cdxml:SUCCEED
pathway4.cdxml:SUCCEED
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3 changes: 3 additions & 0 deletions api/tests/integration/ref/formats/rxn_to_ket.py.out
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@@ -0,0 +1,3 @@
*** RXN to KET ***
2485-bad-layout.ket:SUCCEED
2531-bad-layout.ket:SUCCEED
1 change: 1 addition & 0 deletions api/tests/integration/ref/reaction/pathway.py.out
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Expand Up @@ -8,3 +8,4 @@ pathway7.rdf:SUCCEED
pathway8.rdf:SUCCEED
pathway9.rdf:SUCCEED
pathway10.rdf:SUCCEED
pathway11.rdf:SUCCEED
1 change: 1 addition & 0 deletions api/tests/integration/tests/formats/ket_cdxml.py
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Expand Up @@ -28,6 +28,7 @@ def find_diff(a, b):
"multi_overlap",
"961-text_size",
"generic",
"2558-missed",
]

files.sort()
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1 change: 1 addition & 0 deletions api/tests/integration/tests/formats/ket_to_rdf.py
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Expand Up @@ -36,6 +36,7 @@ def find_diff(a, b):
"pathway8",
"pathway9",
"pathway10",
"pathway11",
]

files.sort()
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1 change: 1 addition & 0 deletions api/tests/integration/tests/formats/rdf_to_cdxml.py
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Expand Up @@ -33,6 +33,7 @@ def find_diff(a, b):
"pathway8",
"pathway9",
"pathway10",
"pathway11",
]

files.sort()
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65 changes: 65 additions & 0 deletions api/tests/integration/tests/formats/reactions/2485-bad-layout.rxn
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$RXN V3000

-INDIGO- 1021241118

M V30 COUNTS 2 1
M V30 BEGIN REACTANT
M V30 BEGIN CTAB
M V30 COUNTS 5 5 0 0 0
M V30 BEGIN ATOM
M V30 1 C -29.801 19.8069 0.0 0
M V30 2 C -29.3006 18.2668 0.0 0
M V30 3 C -28.9913 19.213 0.0 0
M V30 4 C -30.3014 18.2668 0.0 0
M V30 5 C -30.6107 19.213 0.0 0
M V30 END ATOM
M V30 BEGIN BOND
M V30 1 1 1 5
M V30 2 2 5 4
M V30 3 1 4 2
M V30 4 2 2 3
M V30 5 1 3 1
M V30 END BOND
M V30 END CTAB
M V30 BEGIN CTAB
M V30 COUNTS 6 6 0 0 0
M V30 BEGIN ATOM
M V30 1 C -29.6854 16.8444 0.0 0
M V30 2 C -27.9551 16.8449 0.0 0
M V30 3 C -28.8186 17.3445 0.0 0
M V30 4 C -27.9551 15.844 0.0 0
M V30 5 C -29.6854 15.8395 0.0 0
M V30 6 C -28.8164 15.3445 0.0 0
M V30 END ATOM
M V30 BEGIN BOND
M V30 1 2 3 1
M V30 2 1 1 5
M V30 3 2 5 6
M V30 4 1 6 4
M V30 5 2 4 2
M V30 6 1 2 3
M V30 END BOND
M V30 END CTAB
M V30 END REACTANT
M V30 BEGIN PRODUCT
M V30 BEGIN CTAB
M V30 COUNTS 6 6 0 0 0
M V30 BEGIN ATOM
M V30 1 C -23.9637 16.744 0.0 0
M V30 2 C -24.6708 17.4511 0.0 0
M V30 3 C -24.412 18.417 0.0 0
M V30 4 C -23.446 18.6758 0.0 0
M V30 5 C -22.7389 17.9687 0.0 0
M V30 6 C -22.9978 17.0028 0.0 0
M V30 END ATOM
M V30 BEGIN BOND
M V30 1 1 2 1
M V30 2 1 3 2
M V30 3 1 4 3
M V30 4 1 5 4
M V30 5 1 6 5
M V30 6 1 1 6
M V30 END BOND
M V30 END CTAB
M V30 END PRODUCT
M END
113 changes: 113 additions & 0 deletions api/tests/integration/tests/formats/reactions/2531-bad-layout.rxn
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@@ -0,0 +1,113 @@
$RXN

RDKit

1 1
$MOL

RDKit 2D

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M END
$MOL

RDKit 2D

19 19 0 0 0 0 0 0 0 0999 V2000
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