Merge pull request #30 from paulsaxe/main

Fixed problem with Alembic

.github/workflows/BranchCI.yaml

@@ -35,7 +35,7 @@ jobs:
     - name: Run linters
       shell: bash -l {0}
       run: |
-        black --check --diff --extend-exclude '_version.py' seamm_datastore
+        black --check --diff --extend-exclude '_version.py|alembic/' seamm_datastore
         flake8 seamm_datastore
     - name: Run tests
       shell: bash -l {0}

.github/workflows/CI.yaml

@@ -43,7 +43,7 @@ jobs:
     - name: Run linters
       shell: bash -l {0}
       run: |
-        black --check --diff  --extend-exclude '_version.py' seamm_datastore
+        black --check --diff  --extend-exclude '_version.py|alembic/' seamm_datastore
         flake8 seamm_datastore
   test:
     name: Test on ${{ matrix.os }}, Python ${{ matrix.python-version }}

.github/workflows/Release.yaml

@@ -36,7 +36,7 @@ jobs:
     - name: Run linters
       shell: bash -l {0}
       run: |
-        black --check --diff  --extend-exclude '_version.py' seamm_datastore
+        black --check --diff  --extend-exclude '_version.py|alembic/' seamm_datastore
         flake8 seamm_datastore
 
   test:

Makefile

@@ -50,11 +50,11 @@ clean-test: ## remove test and coverage artifacts
 	find . -name '.pytype' -exec rm -fr {} +
 
 lint: ## check style with black and flake8
-	black --check --diff --extend-exclude '_version.py' $(MODULE)
+	black --check --diff --extend-exclude '_version.py|alembic/' $(MODULE)
 	flake8 $(MODULE)
 
 format: ## reformat with black
-	black --extend-exclude '_version.py' $(MODULE)
+	black --extend-exclude '_version.py|alembic/' $(MODULE)
 
 typing: ## check typing
 	pytype $(MODULE)

seamm_datastore/database/alembic/versions/7b24598d1fee_remove_path_add_flowchart_metadata_.py

@@ -5,7 +5,6 @@
 Create Date: 2022-03-24 19:20:10.341379
 
 """
-
 from alembic import op
 import sqlalchemy as sa
 
@@ -19,11 +18,20 @@
 
 def upgrade():
     # ### commands auto generated by Alembic - please adjust! ###
-    op.add_column("flowcharts", sa.Column("conceptdoi", sa.Text(), nullable=True))
-    op.add_column(
-        "flowcharts", sa.Column("flowchart_metadata", sa.JSON(), nullable=True)
-    )
-    op.drop_column("flowcharts", "path")
+    try:
+        op.add_column("flowcharts", sa.Column("conceptdoi", sa.Text(), nullable=True))
+    except Exception:
+        pass
+    try:
+        op.add_column(
+            "flowcharts", sa.Column("flowchart_metadata", sa.JSON(), nullable=True)
+        )
+    except Exception:
+        pass
+    try:
+        op.drop_column("flowcharts", "path")
+    except Exception:
+        pass
     # ### end Alembic commands ###