Config refactor

CMakeLists.txt

@@ -6,6 +6,7 @@ find_package(pybind11 CONFIG REQUIRED)
 
 # emodlib src files
 set(EMODLIB_OBJECTS
+    ${CMAKE_SOURCE_DIR}/include/emodlib/malaria/MalariaConfig.cpp
     ${CMAKE_SOURCE_DIR}/include/emodlib/malaria/InfectionMalaria.cpp
     ${CMAKE_SOURCE_DIR}/include/emodlib/malaria/SusceptibilityMalaria.cpp
     ${CMAKE_SOURCE_DIR}/include/emodlib/malaria/IntrahostComponent.cpp

MIGRATION.md

@@ -0,0 +1,149 @@
+# Migration Guide: v0.0.4 to v0.1.0
+
+## Breaking Changes
+
+Version 0.1.0 introduces a thread-safe, instance-based configuration system. The previous static configuration pattern has been removed.
+
+### Configuration API Changes
+
+**v0.0.4 (Old)**
+```python
+from emodlib.malaria import IntrahostComponent
+
+# Set params globally (affected all instances)
+IntrahostComponent.set_params({'Run_Number': 42})
+IntrahostComponent.update_params({'infection_params': {'Antigen_Switch_Rate': 1e-9}})
+
+# Create instance (used global params)
+ic = IntrahostComponent.create()
+```
+
+**v0.1.0 (New)**
+```python
+from emodlib.malaria import IntrahostComponent, create_config
+
+# Create config instance (thread-safe, independent)
+config = create_config({'Run_Number': 42})
+
+# Or with nested params
+config = create_config({
+    'Run_Number': 42,
+    'infection_params': {'Antigen_Switch_Rate': 1e-9}
+})
+
+# Create instance with config
+ic = IntrahostComponent.create(config)
+```
+
+### Removed Functions
+
+| Removed | Replacement |
+|---------|-------------|
+| `IntrahostComponent.set_params(params)` | `config = create_config(params)` |
+| `IntrahostComponent.update_params(params)` | `config.update(params)` |
+| `IntrahostComponent.params` | `config.yaml` or config properties |
+
+### Incremental Updates with config.update()
+
+The `update()` method provides the same incremental merge behavior as the old `update_params()`:
+
+```python
+# Create config with initial params
+config = create_config({'Run_Number': 1, 'Max_Individual_Infections': 3})
+
+# Later, update just one param (keeps Run_Number=1, Max_Individual_Infections=3)
+config.update({'infection_params': {'Antigen_Switch_Rate': 1e-8}})
+
+# Method chaining also works
+config.update({'Run_Number': 2}).update({'infection_params': {'Antigen_Switch_Rate': 1e-9}})
+```
+
+### Creating Susceptibility and Infection Objects
+
+**v0.0.4**
+```python
+from emodlib.malaria import Susceptibility, Infection
+
+s = Susceptibility.create()
+inf = Infection.create(susceptibility=s, hepatocytes=1)
+```
+
+**v0.1.0**
+```python
+from emodlib.malaria import Susceptibility, Infection, create_config
+
+config = create_config()
+s = Susceptibility.create(config)
+inf = Infection.create(susceptibility=s, config=config, hepatocytes=1)
+```
+
+### Viewing Configuration
+
+**v0.0.4**
+```python
+print(IntrahostComponent.params.yaml)
+```
+
+**v0.1.0**
+```python
+config = create_config()
+print(config.yaml)
+```
+
+### Multi-Simulation Workflows
+
+**v0.0.4** - Simulations with different parameters required careful sequencing:
+```python
+IntrahostComponent.set_params({'Run_Number': 1})
+ic1 = IntrahostComponent.create()
+
+IntrahostComponent.set_params({'Run_Number': 2})  # Changed global state!
+ic2 = IntrahostComponent.create()
+```
+
+**v0.1.0** - Each config is independent (thread-safe):
+```python
+config1 = create_config({'Run_Number': 1})
+config2 = create_config({'Run_Number': 2})
+
+ic1 = IntrahostComponent.create(config1)
+ic2 = IntrahostComponent.create(config2)
+
+# Can run in parallel without interference
+```
+
+## Quick Migration Checklist
+
+1. Add `create_config` to imports:
+   ```python
+   from emodlib.malaria import IntrahostComponent, create_config
+   ```
+
+2. Replace `set_params()` with `create_config()`:
+   ```python
+   # Before
+   IntrahostComponent.set_params({'Run_Number': 42})
+
+   # After
+   config = create_config({'Run_Number': 42})
+   ```
+
+3. Replace `update_params()` with `config.update()`:
+   ```python
+   # Before
+   IntrahostComponent.update_params({'infection_params': {'X': 1}})
+
+   # After
+   config.update({'infection_params': {'X': 1}})
+   ```
+
+4. Pass config to `create()`:
+   ```python
+   # Before
+   ic = IntrahostComponent.create()
+
+   # After
+   ic = IntrahostComponent.create(config)
+   ```
+
+5. For `Susceptibility.create()` and `Infection.create()`, add config parameter.

docs/tutorials/tut_challenge.ipynb

@@ -10,40 +10,17 @@
   },
   {
    "cell_type": "code",
-   "execution_count": 1,
+   "execution_count": null,
    "metadata": {},
    "outputs": [],
-   "source": [
-    "import numpy as np\n",
-    "import pandas as pd\n",
-    "import matplotlib.pyplot as plt\n",
-    "\n",
-    "from emodlib.malaria import IntrahostComponent"
-   ]
+   "source": "import numpy as np\nimport pandas as pd\nimport matplotlib.pyplot as plt\n\nfrom emodlib.malaria import IntrahostComponent, create_config"
   },
   {
    "cell_type": "code",
-   "execution_count": 2,
+   "execution_count": null,
    "metadata": {},
    "outputs": [],
-   "source": [
-    "duration = 300\n",
-    "\n",
-    "asexuals = np.zeros(duration)\n",
-    "gametocytes = np.zeros(duration)\n",
-    "\n",
-    "ic = IntrahostComponent.create()\n",
-    "ic.challenge()\n",
-    "\n",
-    "for t in range(duration):\n",
-    "    ic.update(dt=1)\n",
-    "    asexuals[t] = ic.parasite_density\n",
-    "    gametocytes[t] = ic.gametocyte_density\n",
-    "\n",
-    "df = pd.DataFrame({'days': range(duration),\n",
-    "                   'parasite_density': asexuals,\n",
-    "                   'gametocyte_density': gametocytes}).set_index('days')"
-   ]
+   "source": "duration = 300\n\nasexuals = np.zeros(duration)\ngametocytes = np.zeros(duration)\n\nconfig = create_config()\nic = IntrahostComponent.create(config)\nic.challenge()\n\nfor t in range(duration):\n    ic.update(dt=1)\n    asexuals[t] = ic.parasite_density\n    gametocytes[t] = ic.gametocyte_density\n\ndf = pd.DataFrame({'days': range(duration),\n                   'parasite_density': asexuals,\n                   'gametocyte_density': gametocytes}).set_index('days')"
   },
   {
    "cell_type": "code",
@@ -205,4 +182,4 @@
  },
  "nbformat": 4,
  "nbformat_minor": 2
-}
+}