From acadb61f4cc51a8095ece5be472db4bf5f839131 Mon Sep 17 00:00:00 2001
From: Francois Colleoni <110899888+inoelloc@users.noreply.github.com>
Date: Fri, 12 Jul 2024 12:11:01 +0200
Subject: [PATCH] Rebase of MJA pull request on main (#241) (#245)

---
 smash/_constant.py                    |  5 +++++
 smash/core/model/_standardize.py      | 18 ++++++++++++------
 smash/core/simulation/_standardize.py | 15 ++++++++-------
 venv_install.sh                       | 20 +++++---------------
 4 files changed, 30 insertions(+), 28 deletions(-)

diff --git a/smash/_constant.py b/smash/_constant.py
index a7304ab1..928b067c 100644
--- a/smash/_constant.py
+++ b/smash/_constant.py
@@ -29,6 +29,11 @@ def get_rr_states_from_structure(structure: str) -> list[str]:
     return rr_states
 
 
+### FLOAT PRECISION FOR FLOAT COMPARISON ###
+F_PRECISION = 1.0e-5
+############################################
+
+
 ### MODULE ###
 ##############
 
diff --git a/smash/core/model/_standardize.py b/smash/core/model/_standardize.py
index e69ecf17..ef68e75f 100644
--- a/smash/core/model/_standardize.py
+++ b/smash/core/model/_standardize.py
@@ -10,6 +10,7 @@
 
 from smash._constant import (
     DEFAULT_MODEL_SETUP,
+    F_PRECISION,
     FEASIBLE_RR_INITIAL_STATES,
     FEASIBLE_RR_PARAMETERS,
     FEASIBLE_SERR_MU_PARAMETERS,
@@ -32,11 +33,16 @@
     from smash.util._typing import AnyTuple, ListLike, Numeric
 
 
-def _standardize_model_setup_bool(key: str, value: bool) -> bool:
-    if not isinstance(value, bool):
-        raise TypeError(f"{key} model setup must be a boolean")
+def _standardize_model_setup_bool(key: str, value: bool | int) -> bool:
+    if isinstance(value, bool):
+        pass
+    elif isinstance(value, int):
+        if value not in (0, 1):
+            raise ValueError(f"{key} model setup must be equal to 0 or 1")
+    else:
+        raise TypeError(f"{key} model setup must be a boolean or integer (0, 1)")
 
-    return value
+    return bool(value)
 
 
 def _standardize_model_setup_directory(read: bool, key: str, value: str | None) -> str:
@@ -531,7 +537,7 @@ def _standardize_rr_parameters_value(
             f"{value.shape} into shape {model.mesh.flwdir.shape}"
         )
 
-    if low_arr <= low or upp_arr >= upp:
+    if (low_arr + F_PRECISION) <= low or (upp_arr - F_PRECISION) >= upp:
         raise ValueError(
             f"Invalid value for model rr_parameter '{key}'. rr_parameter domain [{low_arr}, {upp_arr}] is "
             f"not included in the feasible domain ]{low}, {upp}["
@@ -557,7 +563,7 @@ def _standardize_rr_states_value(
             f"{value.shape} into shape {model.mesh.flwdir.shape}"
         )
 
-    if low_arr <= low or upp_arr >= upp:
+    if (low_arr + F_PRECISION) <= low or (upp_arr - F_PRECISION) >= upp:
         raise ValueError(
             f"Invalid value for model {state_kind} '{key}'. {state_kind} domain [{low_arr}, {upp_arr}] is "
             f"not included in the feasible domain ]{low}, {upp}["
diff --git a/smash/core/simulation/_standardize.py b/smash/core/simulation/_standardize.py
index 83c57bf1..779efc4b 100644
--- a/smash/core/simulation/_standardize.py
+++ b/smash/core/simulation/_standardize.py
@@ -15,6 +15,7 @@
     DEFAULT_TERMINATION_CRIT,
     EVENT_SEG_KEYS,
     F90_OPTIMIZER_CONTROL_TFM,
+    F_PRECISION,
     FEASIBLE_RR_INITIAL_STATES,
     FEASIBLE_RR_PARAMETERS,
     FEASIBLE_SERR_MU_PARAMETERS,
@@ -107,7 +108,7 @@ def _standardize_simulation_samples(model: Model, samples: Samples) -> Samples:
             arr = getattr(samples, key)
             low_arr = np.min(arr)
             upp_arr = np.max(arr)
-            if low_arr <= low or upp_arr >= upp:
+            if (low_arr + F_PRECISION) <= low or (upp_arr - F_PRECISION) >= upp:
                 raise ValueError(
                     f"Invalid sample values for parameter '{key}'. Sample domain [{low_arr}, {upp_arr}] is "
                     f"not included in the feasible domain ]{low}, {upp}["
@@ -239,13 +240,13 @@ def _standardize_simulation_optimize_options_bounds(
 
         low_arr = np.min(arr)
         upp_arr = np.max(arr)
-        if (low_arr + 1e-3) < value[0] or (upp_arr - 1e-3) > value[1]:
+        if (low_arr + F_PRECISION) < value[0] or (upp_arr - F_PRECISION) > value[1]:
             raise ValueError(
                 f"Invalid bounds values for parameter '{key}'. Bounds domain [{value[0]}, {value[1]}] does "
                 f"not include parameter domain [{low_arr}, {upp_arr}] in bounds optimize_options"
             )
 
-        if value[0] <= low or value[1] >= upp:
+        if (value[0] + F_PRECISION) <= low or (value[1] - F_PRECISION) >= upp:
             raise ValueError(
                 f"Invalid bounds values for parameter '{key}'. Bounds domain [{value[0]}, {value[1]}] is not "
                 f"included in the feasible domain ]{low}, {upp}[ in bounds optimize_options"
@@ -1099,7 +1100,7 @@ def _standardize_simulation_parameters_feasibility(model: Model):
         low_arr = np.min(arr)
         upp_arr = np.max(arr)
 
-        if low_arr <= low or upp_arr >= upp:
+        if (low_arr + F_PRECISION) <= low or (upp_arr - F_PRECISION) >= upp:
             raise ValueError(
                 f"Invalid value for model rr_parameter '{key}'. rr_parameter domain [{low_arr}, {upp_arr}] "
                 f"is not included in the feasible domain ]{low}, {upp}["
@@ -1111,7 +1112,7 @@ def _standardize_simulation_parameters_feasibility(model: Model):
         low_arr = np.min(arr)
         upp_arr = np.max(arr)
 
-        if low_arr <= low or upp_arr >= upp:
+        if (low_arr + F_PRECISION) <= low or (upp_arr - F_PRECISION) >= upp:
             raise ValueError(
                 f"Invalid value for model rr_initial_state '{key}'. rr_initial_state domain "
                 f"[{low_arr}, {upp_arr}] is not included in the feasible domain ]{low}, {upp}["
@@ -1126,7 +1127,7 @@ def _standardize_simulation_parameters_feasibility(model: Model):
         low_arr = np.min(arr)
         upp_arr = np.max(arr)
 
-        if low_arr <= low or upp_arr >= upp:
+        if (low_arr + F_PRECISION) <= low or (upp_arr - F_PRECISION) >= upp:
             raise ValueError(
                 f"Invalid value for model serr_mu_parameter '{key}'. serr_mu_parameter domain "
                 f"[{low_arr}, {upp_arr}] is not included in the feasible domain ]{low}, {upp}["
@@ -1140,7 +1141,7 @@ def _standardize_simulation_parameters_feasibility(model: Model):
         low_arr = np.min(arr)
         upp_arr = np.max(arr)
 
-        if low_arr <= low or upp_arr >= upp:
+        if (low_arr + F_PRECISION) <= low or (upp_arr - F_PRECISION) >= upp:
             raise ValueError(
                 f"Invalid value for model serr_sigma_parameter '{key}'. serr_sigma_parameter domain "
                 f"[{low_arr}, {upp_arr}] is not included in the feasible domain ]{low}, {upp}["
diff --git a/venv_install.sh b/venv_install.sh
index df6dda15..a5bf1887 100755
--- a/venv_install.sh
+++ b/venv_install.sh
@@ -4,7 +4,7 @@
 #When running this script, you will be prompted for your administrator password to install the required dependencies.
 
 venv_path=~/python_venv
-env_name=smash_1.0
+env_name=smash_dev_1.0
 
 
 #Parse input arguments
@@ -51,14 +51,14 @@ fi
 #Warning to the user
 if [ $(cat /etc/*release | grep ^NAME | grep -o Ubuntu) == "Ubuntu" ]; then
 
-    DEB_PACKAGE_NAME="gfortran build-essential gdal-bin libgdal-dev libshp-dev python3-gdal python3-venv python3-dev"
+    DEB_PACKAGE_NAME="gfortran build-essential python3-venv"
     echo "==============================================="
     echo "Make sure you first installed the following package (ubuntu): $DEB_PACKAGE_NAME"
     echo "==============================================="
     
 else
 
-    PACKAGE_NAME="gfortran build-essential gdal-bin libgdal-dev libshp-dev python3-gdal python3-venv python3-dev"
+    PACKAGE_NAME="gfortran build-essential python3-venv python3-dev"
     echo "==============================================="
     echo "Builging smash require some packages. Make sure you install them first. Install the corresponding package depending your distribution. On Debian/Ubuntu these package are: $PACKAGE_NAME"
     echo "==============================================="
@@ -83,10 +83,7 @@ if [ ! -d "${venv_path}/.venv-${env_name}" ] ; then
     
     #install python dependencies
     pip install --upgrade pip
-    pip install 'numpy>=1.13,<=1.23'
-    pip install f90wrap
-    pip install wheel
-    pip install rasterio pandas h5py tqdm scipy pyyaml terminaltables matplotlib
+    pip install -r requirements-dev.txt
     
     echo ''
     echo 'Building Smash...'
@@ -94,12 +91,6 @@ if [ ! -d "${venv_path}/.venv-${env_name}" ] ; then
     
     make
     
-    echo ''
-    echo 'Installing extra-package for building the documentation...'
-    echo ''
-    #install extra-package for building the documentation:
-    pip install sphinx numpydoc pydata-sphinx-theme ipython sphinxcontrib-bibtex sphinx-design sphinx-autosummary-accessors pytest pytest-cov black ruff fprettify
-    
 else
     echo ''
     echo "The python environnemnt ${venv_path}/${env_name} already exist..."
@@ -121,5 +112,4 @@ echo '>Then launch python:'
 echo '(smash)> python'
 echo 'Import the SMASH package in your python shell:'
 echo '>>> import smash'
-echo '************************************************'
-
+echo '************************************************'
\ No newline at end of file