Merge pull request #10 from PGScatalog/refactor-packages

Merge libraries and applications

Author: smlmbrt

.github/workflows/calc-pytest.yml

@@ -0,0 +1,15 @@
+name: Run pytest on pgscatalog.calc
+
+on:
+  push:
+    paths:
+      - 'pgscatalog.calc/**.py'
+  pull_request:
+    paths:
+      - 'pgscatalog.calc/**.py'
+
+jobs:
+  pytest-calc:
+    uses: ./.github/workflows/pytest.yaml
+    with:
+      package-directory: "pgscatalog.calc"

.github/workflows/calcapp-pytest.yml

@@ -0,0 +1,15 @@
+name: Run pytest on pgscatalog.core
+
+on:
+  push:
+    paths:
+      - 'pgscatalog.core/**.py'
+  pull_request:
+    paths:
+      - 'pgscatalog.core/**.py'
+
+jobs:
+  pytest-core:
+    uses: ./.github/workflows/pytest.yaml
+    with:
+      package-directory: "pgscatalog.core"

.github/workflows/calclib-pytest.yml

@@ -1,12 +1,12 @@
-name: Publish corelib
+name: Publish pgscatalog.core
 
 on:
   workflow_dispatch:
     inputs:
       package-directory:
         type: choice
         options:
-          - pgscatalog.corelib
+          - pgscatalog.core
       python-version:
         required: false
         type: choice

.github/workflows/combineapp-pytest.yml

@@ -0,0 +1,15 @@
+name: Run pytest on pgscatalog.match
+
+on:
+  push:
+    paths:
+      - 'pgscatalog.match/**.py'
+  pull_request:
+    paths:
+      - 'pgscatalog.match/**.py'
+
+jobs:
+  pytest-match:
+    uses: ./.github/workflows/pytest.yaml
+    with:
+      package-directory: "pgscatalog.match"

.github/workflows/core-pytest.yml

@@ -34,10 +34,11 @@
 
 # use autoapi for packages that provide APIs (libraries)
 autoapi_dirs = [
-    "../pgscatalog.corelib/src/pgscatalog",
-    "../pgscatalog.matchlib/src/pgscatalog",
-    "../pgscatalog.calclib/src/pgscatalog",
+    "../pgscatalog.core/src/pgscatalog/",
+    "../pgscatalog.match/src/pgscatalog",
+    "../pgscatalog.calc/src/pgscatalog",
 ]
+
 # see _templates/autoapi/index.rst for autoapi fix
 autoapi_template_dir = "_templates/autoapi"
 autoapi_python_use_implicit_namespaces = True
@@ -57,6 +58,8 @@
 def skip_submodules(app, what, name, obj, skip, options):
     if what == "module":
         skip = True
+    if "cli" in name:
+        skip = True
     return skip
 
 

.github/workflows/corelib-publish.yml

@@ -12,7 +12,7 @@ Installation
 
 ::
 
-    $ pip install pgscatalog-calcapp
+    $ pip install pgscatalog-calc
 
 Usage
 -----

.github/workflows/corelib-pytest.yml

@@ -14,7 +14,7 @@ Installation
 
 ::
 
-    $ pip install pgscatalog-calcapp
+    $ pip install pgscatalog-calc
 
 Usage
 -----

.github/workflows/downloadapp-pytest.yml

@@ -19,7 +19,7 @@ Installation
 
 ::
 
-    $ pip install pgscatalog-combine
+    $ pip install pgscatalog-core
 
 Usage
 -----

.github/workflows/match-pytest.yml

@@ -13,7 +13,7 @@ Installation
 
 ::
 
-    $ pip install pgscatalog-download
+    $ pip install pgscatalog-core
 
 Usage
 -----

.github/workflows/matchapp-pytest.yml

@@ -16,7 +16,7 @@ Installation
 
 ::
 
-    $ pip install pgscatalog-matchapp
+    $ pip install pgscatalog-match
 
 Usage
 -----