Merge pull request #1 from DataAnalyticsEngineering/update-documentation

Update documentation
DataAnalyticsEngineering · May 14, 2024 · 93e31a8 · 93e31a8
2 parents a1c321c + c65c9a5
commit 93e31a8
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Showing 9 changed files with 75 additions and 39 deletions.
diff --git a/.github/workflows/ci.yml b/.github/workflows/ci.yml
@@ -63,12 +63,17 @@ jobs:
         uses: actions/setup-python@v5
         with:
           python-version: ${{ matrix.python-version }}
+      - name: Install pandoc
+        #uses: docker://pandoc/core:2.9
+        run: |
+          sudo apt update
+          sudo apt install pandoc -y
       - name: Install thermontfa
         run: pip install .[dev]
       - name: Build documentation
         run: |
           cd docs
-          make html
+          TZ=UTC make html
       - name: Upload artifacts
         uses: actions/upload-artifact@v4
         with:

diff --git a/docs/conf.py b/docs/conf.py
@@ -24,10 +24,10 @@
     "sphinx.ext.autosectionlabel",
     "nbsphinx",
     "sphinx_gallery.load_style",
-    "nbsphinx_link",
 ]
 myst_enable_extensions = ["dollarmath", "amsmath"]
 nbsphinx_allow_errors = True
+autodoc_member_order = "bysource"
 
 templates_path = ["_templates"]
 exclude_patterns = ["build", "Thumbs.db", ".DS_Store"]

diff --git a/docs/examples.rst b/docs/examples.rst
@@ -2,10 +2,10 @@ Examples
 --------
 
 .. nbgallery::
-   examples/material_parameters.nblink
-   examples/truncate_ntfa_modes.nblink
-   examples/paper_plots.nblink
-   examples/generate_inputs.nblink
-   examples/generate_plots.nblink
-   examples/NTFA_thermo_paper.nblink
-   examples/thermoNTFA_example.nblink
+   examples/material_parameters
+   examples/truncate_ntfa_modes
+   examples/paper_plots
+   examples/generate_inputs
+   examples/generate_plots
+   examples/NTFA_thermo_paper
+   examples/thermoNTFA_example
diff --git a/docs/index.rst b/docs/index.rst
@@ -14,10 +14,10 @@ TODO: abstract
    :maxdepth: 2
    :caption: Contents:
 
-   Workflow<workflow>
-   Installation<installation>
-   ThermoNTFA Documentation<api>
-   Examples<examples>
+   workflow
+   installation
+   api
+   examples
    MarkdownLinks/license
    MarkdownLinks/citation
    MarkdownLinks/changelog

diff --git a/examples/paper_plots.ipynb b/examples/paper_plots.ipynb
@@ -25,11 +25,7 @@
     "> Felix Fritzen is funded by the German Research Foundation (DFG) --\n",
     "> 390740016 (EXC-2075); 406068690 (FR2702/8-1); 517847245 (FR2702/10-1).\n",
     "\n",
-    "## Mode study\n",
-    "## Training reproduction tests\n",
-    "## Random loading\n",
-    "## Stress-driven simulation\n",
-    "## Twoscale simulation"
+    "## Imports:"
    ]
   },
   {
@@ -80,6 +76,18 @@
     "        )"
    ]
   },
+  {
+   "cell_type": "markdown",
+   "id": "bd108d2a",
+   "metadata": {},
+   "source": [
+    "## Mode study\n",
+    "## Training reproduction tests\n",
+    "## Random loading\n",
+    "## Stress-driven simulation\n",
+    "## Twoscale simulation"
+   ]
+  },
   {
    "cell_type": "markdown",
    "id": "9ef6456e",
@@ -785,6 +793,18 @@
     "            GG.create_dataset(\"xi\", data=xi)"
    ]
   },
+  {
+   "cell_type": "markdown",
+   "id": "46edb92e",
+   "metadata": {},
+   "source": [
+    "1. set the stress to 0\n",
+    "2. ramp the temperature from 293K\n",
+    "3. check for q >= q_crit_0, q_crit_1, ...\n",
+    "   e.g. q_crit_0 = 0.002 (i.e. 0.2%)\n",
+    "4. draw the results of theta"
+   ]
+  },
   {
    "cell_type": "code",
    "execution_count": null,
@@ -794,12 +814,6 @@
    },
    "outputs": [],
    "source": [
-    "# 1. set the stress to 0\n",
-    "# 2. ramp the temperature from 293K\n",
-    "# 3. check for q >= q_crit_0, q_crit_1, ...\n",
-    "#    e.g. q_crit_0 = 0.002 (i.e. 0.2%)\n",
-    "# draw the results of theta\n",
-    "\n",
     "n_ramp = 1300 - 293 + 1\n",
     "with h5py.File(\"ms9p_thermal_rampup.h5\", \"w\") as F:\n",
     "    eps_idx = None\n",

diff --git a/examples/paper_plots.py b/examples/paper_plots.py
@@ -35,11 +35,7 @@
 # > Felix Fritzen is funded by the German Research Foundation (DFG) --
 # > 390740016 (EXC-2075); 406068690 (FR2702/8-1); 517847245 (FR2702/10-1).
 #
-# ## Mode study
-# ## Training reproduction tests
-# ## Random loading
-# ## Stress-driven simulation
-# ## Twoscale simulation
+# ## Imports:
 
 # %%
 import os
@@ -83,6 +79,13 @@ def rel_error(A, A_ref, r_min=None):
         )
 
 
+# %% [markdown]
+# ## Mode study
+# ## Training reproduction tests
+# ## Random loading
+# ## Stress-driven simulation
+# ## Twoscale simulation
+
 # %% [markdown]
 # **Load the NTFA data**
 
@@ -612,13 +615,14 @@ def rel_error(A, A_ref, r_min=None):
             GG.create_dataset("xi", data=xi)
 
 
-# %% Figuring when palsticity kicks in using the mixed UMAT
+# %% [markdown]
 # 1. set the stress to 0
 # 2. ramp the temperature from 293K
 # 3. check for q >= q_crit_0, q_crit_1, ...
 #    e.g. q_crit_0 = 0.002 (i.e. 0.2%)
-# draw the results of theta
+# 4. draw the results of theta
 
+# %% Figuring when palsticity kicks in using the mixed UMAT
 n_ramp = 1300 - 293 + 1
 with h5py.File("ms9p_thermal_rampup.h5", "w") as F:
     eps_idx = None

diff --git a/pyproject.toml b/pyproject.toml
@@ -28,13 +28,15 @@ dependencies = [
 
 [project.optional-dependencies]
 dev = [
-    'jupytext~=1.16.1',
-    'jupyterlab~=4.1.8',
-    'pre_commit~=3.7.0',
-    'pytest',
+    'jupyterlab~=4.2.0',
+    'jupytext~=1.16.2',
+    'pre-commit~=3.7.1',
+    'pytest~=8.2.0',
     'sphinx',
-    'myst_parser',
-    'sphinx_rtd_theme'
+    'myst-parser~=3.0.1',
+    'nbsphinx~=0.9.4',
+    'sphinx-gallery~=0.16.0',
+    'sphinx-rtd-theme~=2.0.0'
 ]
 
 [tool.flake8]

diff --git a/thermontfa/tabular_interpolation.py b/thermontfa/tabular_interpolation.py
@@ -1,7 +1,7 @@
 #!/usr/bin/env python3
 # -*- coding: utf-8 -*-
 """
-Tabular interpolation for the NTFA
+Tabular interpolation for the thermo-mechanical NTFA
 
 (c) 2024,
 Felix Fritzen <fritzen@simtech.uni-stuttgart.de>,

diff --git a/thermontfa/thermoNTFA.py b/thermontfa/thermoNTFA.py
@@ -22,7 +22,7 @@
 390740016 (EXC-2075); 406068690 (FR2702/8-1); 517847245 (FR2702/10-1).
 """
 
-from typing import Callable, Optional, Tuple
+from typing import Callable, Optional, Tuple, List
 
 import h5py
 import numpy as np
@@ -39,6 +39,17 @@ class ThermoMechNTFA:
     """
 
     # TODO: Document properties
+    file_name: str
+    group_name: str
+    sig_y: Callable[[float, float, bool], float]
+    tol: float
+    verbose: bool = False
+    A_bar: TabularInterpolation
+    C_bar: TabularInterpolation
+    D_xi: TabularInterpolation
+    tau_theta: TabularInterpolation
+    tau_xi: TabularInterpolation
+    sig_phases: List
 
     def __init__(
         self,