Vb/db

.github/workflows/test_unpinned_deps.yml

@@ -30,9 +30,9 @@ jobs:
 
     - name: Install package with dev deps
       run: |
-        uv pip install -e .[dev]
+        uv pip install .[dev]
         uv pip freeze
 
     - name: Pytest
       run: |
-        uv run python -m pytest
+        uv run --no-project python -m pytest

CMakeLists.txt

@@ -24,6 +24,18 @@ add_subdirectory(${IPHREEQC_DIR} ${IPHREEQC_BUILD_DIR})
 set_target_properties(IPhreeqc PROPERTIES POSITION_INDEPENDENT_CODE ON)
 # -------------------------------------------------------
 
+# -------------------------------------------------------
+# IPhreeqc databases
+# -------------------------------------------------------
+# Till we find a way to extract artifacts from IPhreeqc's install folder
+# through scikit-build-core, we define a COMPONENT that allows us to
+# copy the database files.
+set(IPHREEQC_DATABASE_DIR   ${IPHREEQC_BASE}/database)
+install(DIRECTORY
+      "${IPHREEQC_DATABASE_DIR}"
+      DESTINATION pyphreeqc COMPONENT iphreeqc_database)
+# -------------------------------------------------------
+
 include_directories(${IPHREEQC_INCLUDE_DIRS})
 
 pybind11_add_module(_bindings src/bindings.cpp)

src/pyphreeqc/interface.py

@@ -1,4 +1,5 @@
 from typing import Any
+from pathlib import Path
 from pyphreeqc._bindings import PyVar, PY_VAR_TYPE, PY_VRESULT, PyIPhreeqc
 
 IPhreeqc = PyIPhreeqc
@@ -52,8 +53,13 @@ def value(self, value) -> None:
 
 
 class Phreeqc:
-    def __init__(self):
+    def __init__(self, database: str = "phreeqc.dat", database_directory: Path | None = None):
         self._ext = PyIPhreeqc()
+
+        if database_directory is None:
+            database_directory = Path(__file__).parent / "database"
+        self._ext.load_database(str(database_directory / database))
+
         # TODO: Is VAR the common denominator for most operations?
         # Here we create one and modify it in operations instead of having
         # the caller create new VARs per operation.

tests/test_phreeqc.py

@@ -3,15 +3,21 @@
 from pyphreeqc.interface import Phreeqc
 
 
-def test_load_database():
-    phreeqc = Phreeqc()
-    phreeqc.load_database(str(Path(__file__).parent / "phreeqc.dat"))
+def test_load_database_internal():
+    # `phreeqc.dat` is included with the package, so we don't need to specify
+    # `database_directory`.
+    phreeqc = Phreeqc(database="phreeqc.dat")
+
+
+def test_load_database_external():
+    # We can always load an external database by specifying
+    # `database_directory`.
+    phreeqc = Phreeqc(database="phreeqc.dat", database_directory=Path(__file__).parent)
 
 
 def test_run():
     # TODO: Break this down into individual tests
-    phreeqc = Phreeqc()
-    phreeqc.load_database(str(Path(__file__).parent / "phreeqc.dat"))
+    phreeqc = Phreeqc("phreeqc.dat")
 
     phreeqc.run_string("""
         TITLE Example 11.--Transport and ion exchange.