V0.4 Compatible with Hdf5 result V6

.github/workflows/CI.yml

@@ -40,7 +40,7 @@ jobs:
       - uses: actions/checkout@v4
       - uses: actions/setup-python@v5
         with:
-          python-version: 3.x
+          python-version: 3.12
       - name: Install system dependencies
         run: |
           sudo apt-get update

.github/workflows/pages.yml

@@ -0,0 +1,38 @@
+name: Deploy Documentation
+permissions:
+  contents: write
+on:
+  push:
+    branches: [ main ] 
+  pull_request:
+    branches: [ main ]
+
+
+jobs:
+  deploy:
+    runs-on: ubuntu-latest
+    steps:
+      - uses: actions/checkout@v4
+
+      - name: Install system dependencies
+        run: |
+          sudo apt-get update
+          sudo apt-get install -y cmake libhdf5-dev
+
+      - name: Install Rust
+        uses: actions-rs/toolchain@v1
+        with:
+          toolchain: stable
+          profile: minimal
+          override: true
+
+      - name: Generate Documentation
+        run: cargo doc --workspace --no-deps --document-private-items
+
+      - name: Deploy Docs
+        uses: peaceiris/actions-gh-pages@v4
+        with:
+          github_token: ${{ secrets.GITHUB_TOKEN }}
+          publish_branch: gh-pages
+          publish_dir: ./target/doc
+          force_orphan: true

Cargo.toml

@@ -7,7 +7,7 @@ members = [
 resolver = "2"
 
 [workspace.package]
-version = "0.3.4"
+version = "0.4.4"
 edition = "2021"
 license = "MIT"
 repository = "https://github.com/Benncs/BioMC_PostProcess/"

README.md

@@ -3,7 +3,7 @@
 
 
 ## Project Overview
-The **BioMC Postprocessor API** is a Rust module designed to facilitate interaction with post-processing simulation results via the BiomC API.  
+The **BioMC Postprocessor API** is a Rust API designed to interact with and perform post-processing on simulation results obtained with the [BioMC code](https://github.com/Benncs/BioCMA-MCST).  
 It also includes **PyO3 bindings** to provide a high-level Python API for end users.
 
 
@@ -35,3 +35,4 @@ It also includes **PyO3 bindings** to provide a high-level Python API for end us
 ### LICENSE 
 
 
+This code is under [MIT](./LICENSE) license

biomc_pp/rtd.py

@@ -0,0 +1,39 @@
+import biomc_pp 
+import numpy as np 
+import matplotlib.pyplot as plt 
+
+def get_rtd_from_scalar(pp,time,step_concentration):
+
+    c = pp.get_spatial_average_concentration(0,biomc_pp.Phase.Liquid)
+    c0 = c[0]
+    delta_c = c - c0
+    step_concentration = 5
+
+    # Cumulative probability 
+    f_rtd = delta_c / step_concentration  
+    # By defintion F(t)=integral 0 to t (E(t))
+    e_rtd = np.diff(f_rtd) / np.diff(time)
+
+    return f_rtd,e_rtd
+
+def get_rtd_particle(pp):
+    probes = pp.get_probes()/3600
+    return np.histogram(probes, bins=100,density=True)
+
+def plot_rtd(pp,time,step_concentration):
+
+    f_rtd,e_rtd = get_rtd_from_scalar(pp,time,step_concentration)
+    plt.figure()
+    plt.plot(time[1:],e_rtd,'--',color='red',label='Scalar')
+    c,e = get_rtd_particle(pp)
+    plt.bar(
+        e[:-1],
+        c,
+        width=np.diff(e),
+        edgecolor="black",
+        alpha=0.7,
+        color="blue",
+        label="Particles"
+    )
+    return f_rtd,e_rtd
+

core/Cargo.toml

@@ -12,8 +12,11 @@ authors.workspace = true
 publish = true
 
 [dependencies]
+csv = "1.3.1"
 hdf5 = "0.8.1"
 ndarray = "0.16.1"
+serde = { version = "1.0.219", features = ["derive"] }
+serde_json = "1.0.140"
 thiserror = "2.0.11"
 #hdf5-sys = { version = "0.8.1", features = ["static"] }