From bb8fd3ba0204ded37c0308290cb5aa8e56981b2f Mon Sep 17 00:00:00 2001 From: Lucian Smith Date: Tue, 25 Jul 2023 15:38:34 -0700 Subject: [PATCH 1/6] Fix synthetic changes. When read in from an actual SED-ML file, biosimulators_utils assigns the parent model ID to the model's child changes. (This is in support of handling many changes at once, so we know which change came from which model.) This fixes the test itself to duplicate that effect. --- biosimulators_test_suite/test_case/sedml.py | 7 ++++++- 1 file changed, 6 insertions(+), 1 deletion(-) diff --git a/biosimulators_test_suite/test_case/sedml.py b/biosimulators_test_suite/test_case/sedml.py index 975f140..5d6f589 100644 --- a/biosimulators_test_suite/test_case/sedml.py +++ b/biosimulators_test_suite/test_case/sedml.py @@ -309,7 +309,9 @@ def build_synthetic_archives(self, specifications, curated_archive, curated_arch new_value=value, ) ) - + for mod in [model_1, model_2]: + for change in mod: + change.model = mod.id n_children = {} for child in node.getchildren(): _, _, _, child_target, _ = get_xml_node_namespace_tag_target( @@ -448,6 +450,9 @@ def build_synthetic_archives(self, specifications, curated_archive, curated_arch new_value=value, ) ) + for mod in [model_1, model_2]: + for change in mod: + change.model = mod.id n_children = {} for child in node.getchildren(): From 2dcc03beee080fd92364291c9bde334bdbbf7ff2 Mon Sep 17 00:00:00 2001 From: Lucian Smith Date: Tue, 25 Jul 2023 15:41:02 -0700 Subject: [PATCH 2/6] Update version number. --- biosimulators_test_suite/_version.py | 2 +- 1 file changed, 1 insertion(+), 1 deletion(-) diff --git a/biosimulators_test_suite/_version.py b/biosimulators_test_suite/_version.py index 95a0c62..81cb954 100644 --- a/biosimulators_test_suite/_version.py +++ b/biosimulators_test_suite/_version.py @@ -1 +1 @@ -__version__ = '0.1.87' +__version__ = '0.1.88' From b92efe96b0c3a799c25d0a64d42968292cb82c27 Mon Sep 17 00:00:00 2001 From: Lucian Smith Date: Tue, 25 Jul 2023 15:47:39 -0700 Subject: [PATCH 3/6] Use pip 23.0 --- .github/workflows/ci.yml | 7 ++++--- 1 file changed, 4 insertions(+), 3 deletions(-) diff --git a/.github/workflows/ci.yml b/.github/workflows/ci.yml index e9c8677..96c745c 100644 --- a/.github/workflows/ci.yml +++ b/.github/workflows/ci.yml @@ -49,10 +49,11 @@ jobs: restore-keys: | ${{ runner.os }}-pip- - - name: Install pip and setuptools + - name: Install pip run: | - #python -m pip install --upgrade pip - python -m pip install --upgrade setuptools + python -m pip install pip==23.0.0 + python -m pip install pip==23.0.0 + python -m pip --version - name: Install Java # for pyNeuroML uses: actions/setup-java@v2 From 6f2eb5eeba4bac769c67f0940266a87f4577aea1 Mon Sep 17 00:00:00 2001 From: Lucian Smith Date: Tue, 25 Jul 2023 16:39:48 -0700 Subject: [PATCH 4/6] mod.changes, not mod. --- biosimulators_test_suite/test_case/sedml.py | 4 ++-- 1 file changed, 2 insertions(+), 2 deletions(-) diff --git a/biosimulators_test_suite/test_case/sedml.py b/biosimulators_test_suite/test_case/sedml.py index 5d6f589..0ec0c91 100644 --- a/biosimulators_test_suite/test_case/sedml.py +++ b/biosimulators_test_suite/test_case/sedml.py @@ -310,7 +310,7 @@ def build_synthetic_archives(self, specifications, curated_archive, curated_arch ) ) for mod in [model_1, model_2]: - for change in mod: + for change in mod.changes: change.model = mod.id n_children = {} for child in node.getchildren(): @@ -451,7 +451,7 @@ def build_synthetic_archives(self, specifications, curated_archive, curated_arch ) ) for mod in [model_1, model_2]: - for change in mod: + for change in mod.changes: change.model = mod.id n_children = {} From e9c738a838865874aeb99c11574584c434b35a7c Mon Sep 17 00:00:00 2001 From: Lucian Smith Date: Tue, 25 Jul 2023 22:11:03 -0700 Subject: [PATCH 5/6] Don't only release from a single branch. --- .github/workflows/ci.yml | 1 - 1 file changed, 1 deletion(-) diff --git a/.github/workflows/ci.yml b/.github/workflows/ci.yml index 96c745c..b1593dd 100644 --- a/.github/workflows/ci.yml +++ b/.github/workflows/ci.yml @@ -164,7 +164,6 @@ jobs: uses: actions/checkout@v2 with: fetch-depth: 1 - ref: deploy - name: Configure Git run: | From 5683d1799042245ae8b440e026ef70e382e269cd Mon Sep 17 00:00:00 2001 From: Lucian Smith Date: Tue, 25 Jul 2023 22:26:09 -0700 Subject: [PATCH 6/6] Revert; use 'deploy' after all (sigh). --- .github/workflows/ci.yml | 1 + 1 file changed, 1 insertion(+) diff --git a/.github/workflows/ci.yml b/.github/workflows/ci.yml index b1593dd..a5651f7 100644 --- a/.github/workflows/ci.yml +++ b/.github/workflows/ci.yml @@ -164,6 +164,7 @@ jobs: uses: actions/checkout@v2 with: fetch-depth: 1 + branch: deploy - name: Configure Git run: |