From 71c06aa71253d55786c40535b01bbfdb19835b1b Mon Sep 17 00:00:00 2001
From: Bart Schilperoort <b.schilperoort@esciencecenter.nl>
Date: Thu, 11 Jan 2024 08:03:28 +0100
Subject: [PATCH] Move BMI code to bmi module

---
 Dockerfile                                    |  2 +-
 PyStemmusScope/{ => bmi}/docker_process.py    |  0
 .../{bmi.py => bmi/implementation.py}         |  6 ++---
 PyStemmusScope/{ => bmi}/local_process.py     |  0
 PyStemmusScope/{bmi_utils.py => bmi/utils.py} |  0
 docs/notebooks/BMI_demo.ipynb                 | 27 ++++++++++---------
 6 files changed, 18 insertions(+), 17 deletions(-)
 rename PyStemmusScope/{ => bmi}/docker_process.py (100%)
 rename PyStemmusScope/{bmi.py => bmi/implementation.py} (98%)
 rename PyStemmusScope/{ => bmi}/local_process.py (100%)
 rename PyStemmusScope/{bmi_utils.py => bmi/utils.py} (100%)

diff --git a/Dockerfile b/Dockerfile
index 57889635..6e26a813 100644
--- a/Dockerfile
+++ b/Dockerfile
@@ -27,4 +27,4 @@ WORKDIR /
 ENV STEMMUS_SCOPE ./STEMMUS_SCOPE
 
 # Start grpc4bmi server
-CMD run-bmi-server --name "PyStemmusScope.bmi.StemmusScopeBmi" --port 55555 --debug
+CMD run-bmi-server --name "PyStemmusScope.bmi.implementation.StemmusScopeBmi" --port 55555 --debug
diff --git a/PyStemmusScope/docker_process.py b/PyStemmusScope/bmi/docker_process.py
similarity index 100%
rename from PyStemmusScope/docker_process.py
rename to PyStemmusScope/bmi/docker_process.py
diff --git a/PyStemmusScope/bmi.py b/PyStemmusScope/bmi/implementation.py
similarity index 98%
rename from PyStemmusScope/bmi.py
rename to PyStemmusScope/bmi/implementation.py
index f55c5a24..f301e7ed 100644
--- a/PyStemmusScope/bmi.py
+++ b/PyStemmusScope/bmi/implementation.py
@@ -8,7 +8,7 @@
 import h5py
 import numpy as np
 from bmipy.bmi import Bmi
-from PyStemmusScope.bmi_utils import InapplicableBmiMethods
+from PyStemmusScope.bmi.utils import InapplicableBmiMethods
 from PyStemmusScope.config_io import read_config
 
 
@@ -176,7 +176,7 @@ def load_process(mode: Literal["exe", "docker"]) -> type[StemmusScopeProcess]:
     """Load the right STEMMUS_SCOPE process."""
     if mode == "docker":
         try:
-            from PyStemmusScope.docker_process import StemmusScopeDocker as Process
+            from PyStemmusScope.bmi.docker_process import StemmusScopeDocker as Process
         except ImportError as err:
             msg = (
                 "The docker python package is not available."
@@ -184,7 +184,7 @@ def load_process(mode: Literal["exe", "docker"]) -> type[StemmusScopeProcess]:
             )
             raise ImportError(msg) from err
     elif mode == "exe":
-        from PyStemmusScope.local_process import LocalStemmusScope as Process
+        from PyStemmusScope.bmi.local_process import LocalStemmusScope as Process
     else:
         msg = "Unknown mode."
         raise ValueError(msg)
diff --git a/PyStemmusScope/local_process.py b/PyStemmusScope/bmi/local_process.py
similarity index 100%
rename from PyStemmusScope/local_process.py
rename to PyStemmusScope/bmi/local_process.py
diff --git a/PyStemmusScope/bmi_utils.py b/PyStemmusScope/bmi/utils.py
similarity index 100%
rename from PyStemmusScope/bmi_utils.py
rename to PyStemmusScope/bmi/utils.py
diff --git a/docs/notebooks/BMI_demo.ipynb b/docs/notebooks/BMI_demo.ipynb
index 393d93a4..61c47e96 100644
--- a/docs/notebooks/BMI_demo.ipynb
+++ b/docs/notebooks/BMI_demo.ipynb
@@ -17,8 +17,8 @@
    "metadata": {},
    "outputs": [],
    "source": [
-    "#cfg_file = \"/home/bart/tmp/stemmus_scope/config_docker.txt\"\n",
-    "cfg_file = \"/home/bart/tmp/stemmus_scope/config_exe.txt\""
+    "cfg_file = \"/home/bart/tmp/stemmus_scope/config_docker.txt\"\n",
+    "# cfg_file = \"/home/bart/tmp/stemmus_scope/config_exe.txt\""
    ]
   },
   {
@@ -42,7 +42,8 @@
     "        \"/home/bart/matlab_runtime/R2023a/sys/os/glnxa64:\"\n",
     "        \"/home/bart/matlab_runtime/R2023a/extern/bin/glnxa64:\"\n",
     "        \"/home/bart/matlab_runtime/R2023a/sys/opengl/lib/glnxa64\"\n",
-    "    )"
+    "    )\n",
+    "    os.environ[\"STEMMUS_SCOPE\"] = \"/home/bart/Downloads/STEMMUS_SCOPE\""
    ]
   },
   {
@@ -58,7 +59,7 @@
    "metadata": {},
    "outputs": [],
    "source": [
-    "from PyStemmusScope.bmi import StemmusScopeBmi\n",
+    "from PyStemmusScope.bmi.implementation import StemmusScopeBmi\n",
     "from cftime import num2pydate\n",
     "from rich import print\n",
     "import numpy as np\n",
@@ -157,7 +158,7 @@
   },
   {
    "cell_type": "code",
-   "execution_count": 6,
+   "execution_count": 7,
    "metadata": {},
    "outputs": [
     {
@@ -166,7 +167,7 @@
        "array([22.74423625])"
       ]
      },
-     "execution_count": 6,
+     "execution_count": 7,
      "metadata": {},
      "output_type": "execute_result"
     }
@@ -187,7 +188,7 @@
   },
   {
    "cell_type": "code",
-   "execution_count": 7,
+   "execution_count": 8,
    "metadata": {},
    "outputs": [
     {
@@ -221,7 +222,7 @@
   },
   {
    "cell_type": "code",
-   "execution_count": 8,
+   "execution_count": 9,
    "metadata": {},
    "outputs": [],
    "source": [
@@ -254,7 +255,7 @@
   },
   {
    "cell_type": "code",
-   "execution_count": 9,
+   "execution_count": 10,
    "metadata": {},
    "outputs": [],
    "source": [
@@ -271,16 +272,16 @@
   },
   {
    "cell_type": "code",
-   "execution_count": 10,
+   "execution_count": 11,
    "metadata": {},
    "outputs": [
     {
      "data": {
       "text/plain": [
-       "<matplotlib.collections.QuadMesh at 0x7fe86f0ab190>"
+       "<matplotlib.collections.QuadMesh at 0x7f881ab5f010>"
       ]
      },
-     "execution_count": 10,
+     "execution_count": 11,
      "metadata": {},
      "output_type": "execute_result"
     },
@@ -308,7 +309,7 @@
   },
   {
    "cell_type": "code",
-   "execution_count": 11,
+   "execution_count": 6,
    "metadata": {},
    "outputs": [],
    "source": [