ivoryos 1.2.0b1__py3-none-any.whl → 1.2.2__py3-none-any.whl

{ivoryos-1.2.0b1.dist-info → ivoryos-1.2.2.dist-info}/METADATA

@@ -1,11 +1,11 @@
-Metadata-Version: 2.1
+Metadata-Version: 2.4
 Name: ivoryos
-Version: 1.2.0b1
+Version: 1.2.2
 Summary: an open-source Python package enabling Self-Driving Labs (SDLs) interoperability
-Home-page: https://gitlab.com/heingroup/ivoryos
-Author: Ivory Zhang
-Author-email: ivoryzhang@chem.ubc.ca
+Author-email: Ivory Zhang <ivoryzhang@chem.ubc.ca>
 License: MIT
+Project-URL: Homepage, https://gitlab.com/heingroup/ivoryos
+Requires-Python: >=3.7
 Description-Content-Type: text/markdown
 License-File: LICENSE
 Requires-Dist: bcrypt
@@ -17,6 +17,10 @@ Requires-Dist: Flask-WTF
 Requires-Dist: SQLAlchemy-Utils
 Requires-Dist: python-dotenv
 Requires-Dist: astor; python_version < "3.9"
+Provides-Extra: optimizer
+Requires-Dist: ax-platform; extra == "optimizer"
+Requires-Dist: baybe; extra == "optimizer"
+Dynamic: license-file
 
 [![Documentation Status](https://readthedocs.org/projects/ivoryos/badge/?version=latest)](https://ivoryos.readthedocs.io/en/latest/?badge=latest)
 [![PyPI version](https://img.shields.io/pypi/v/ivoryos)](https://pypi.org/project/ivoryos/)
@@ -48,7 +52,7 @@ With the least modification of the current workflow, user can design, manage and
 This software is developed and tested using Windows. This software and its dependencies are compatible across major platforms: Linux, macOS, and Windows. Some dependencies (Flask-SQLAlchemy) may require additional setup.
 
 ### Python Version
-Python >=3.10 for best compatibility. Python >=3.7 without Ax.
+Python >=3.10 for the best compatibility. Python >=3.7 without Ax.
 ### Python dependencies
 This software is compatible with the latest versions of all dependencies. 
 - bcrypt~=4.0
@@ -59,7 +63,9 @@ This software is compatible with the latest versions of all dependencies.
 - SQLAlchemy-Utils~=0.41
 - Flask-WTF~=1.2
 - python-dotenv==1.0.1
-- ax-platform (optional ~=0.4 for Python>=3.9)
+- ax-platform (optional 1.0 for Python>=3.10)
+- baybe (optional)
+
 
 ## Installation
 ```bash
@@ -83,43 +89,60 @@ import ivoryos
 ivoryos.run(__name__)
 ```
 ### Login
-Create an account and login (local database)
+Create an account and login (local database with bcrypt password)
 ### Features
-- **Direct control**: direct function calling _Device_ tab
-- **Workflow design and iteration**:
-  - **Design**: add function to canvas in _Design_ tab. click `Compile and Run` button to go to the execution page
-  - **Execution**: configure iteration methods and parameters in _Compile/Run_ tab. 
-  - **Database**: manage workflows in _Library_ tab.
-- **Info page**: additional info in _About_ tab.
+- **Direct control**: direct function calling _Devices_ tab
+- **Workflows**:
+  - **Design Editor**: drag/add function to canvas in _Design_ tab. click `Compile and Run` button to go to the execution configuration page
+  - **Execution Config**: configure iteration methods and parameters in _Compile/Run_ tab. 
+  - **Design Library**: manage workflow scripts in _Library_ tab.
+  - **Workflow Data**: Execution records are in _Data_ tab.
 
 [//]: # (![Discord]&#40;https://img.shields.io/discord/1313641159356059770&#41;)
 
 [//]: # (![PyPI - Downloads]&#40;https://img.shields.io/pypi/dm/ivoryos&#41;)
 
 
-### Additional settings (not actively maintained)
-#### AI assistant
-To streamline the experimental design on SDLs, we also integrate Large Language Models (LLMs) to interpret the inspected functions and generate code according to task descriptions.
+### Additional settings
+[//]: # (#### AI assistant)
 
-#### Enable LLMs with [OpenAI API](https://github.com/openai/openai-python)
-1. Create a `.env` file for `OPENAI_API_KEY`
-```
-OPENAI_API_KEY="Your API Key"
-```
-2. In your SDL script, define model, you can use any GPT models.
+[//]: # (To streamline the experimental design on SDLs, we also integrate Large Language Models &#40;LLMs&#41; to interpret the inspected functions and generate code according to task descriptions.)
 
-```python
-ivoryos.run(__name__, model="gpt-3.5-turbo")
-```
+[//]: # ()
+[//]: # (#### Enable LLMs with [OpenAI API]&#40;https://github.com/openai/openai-python&#41;)
 
-#### Enable local LLMs with [Ollama](https://ollama.com/)
-1. Download Ollama.
-2. pull models from Ollama
-3. In your SDL script, define LLM server and model, you can use any models available on Ollama.
+[//]: # (1. Create a `.env` file for `OPENAI_API_KEY`)
 
-```python
-ivoryos.run(__name__, llm_server="localhost", model="llama3.1")
-```
+[//]: # (```)
+
+[//]: # (OPENAI_API_KEY="Your API Key")
+
+[//]: # (```)
+
+[//]: # (2. In your SDL script, define model, you can use any GPT models.)
+
+[//]: # ()
+[//]: # (```python)
+
+[//]: # (ivoryos.run&#40;__name__, model="gpt-3.5-turbo"&#41;)
+
+[//]: # (```)
+
+[//]: # ()
+[//]: # (#### Enable local LLMs with [Ollama]&#40;https://ollama.com/&#41;)
+
+[//]: # (1. Download Ollama.)
+
+[//]: # (2. pull models from Ollama)
+
+[//]: # (3. In your SDL script, define LLM server and model, you can use any models available on Ollama.)
+
+[//]: # ()
+[//]: # (```python)
+
+[//]: # (ivoryos.run&#40;__name__, llm_server="localhost", model="llama3.1"&#41;)
+
+[//]: # (```)
 
 #### Add additional logger(s)
 ```python
@@ -144,7 +167,7 @@ ivoryos.run(__name__)
 
  * Running on all addresses (0.0.0.0)
  * Running on http://127.0.0.1:8000
- * Running on http://xxx.xx.xx.xxx:8000
+ * Running on http://0.0.0.0:8000
 
 ### Deck function and web form 
 ![](https://gitlab.com/heingroup/ivoryos/raw/main/docs/source/_static/demo.gif)
@@ -172,6 +195,8 @@ When you run the application for the first time, it will automatically create th
 - [x] dropdown input ✅  
 - [x] show line number option ✅  
 - [ ] snapshot version control
+- [ ] optimizer-agnostic
+- [ ] check batch-config file compatibility
 
 ## Citing
 
@@ -212,4 +237,4 @@ For an additional perspective related to the development of the tool, please see
 ## Authors and Acknowledgement
 Ivory Zhang, Lucy Hao
 
-Authors acknowledge all former and current Hein Lab members for their valuable suggestions. 
+Authors acknowledge Telescope Innovations, Hein Lab members for their valuable suggestions and contributions.

ivoryos-1.2.2.dist-info/RECORD

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+ivoryos/utils/bo_campaign.py,sha256=Fil-zT7JexL_p9XqyWByjAk42XB1R9XUKN8CdV5bi6c,9714
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+ivoryos-1.2.2.dist-info/top_level.txt,sha256=FRIWWdiEvRKqw-XfF_UK3XV0CrnNb6EmVbEgjaVazRM,8
+ivoryos-1.2.2.dist-info/RECORD,,

{ivoryos-1.2.0b1.dist-info → ivoryos-1.2.2.dist-info}/WHEEL

@@ -1,5 +1,5 @@
 Wheel-Version: 1.0
-Generator: bdist_wheel (0.45.1)
+Generator: setuptools (80.9.0)
 Root-Is-Purelib: true
 Tag: py3-none-any
 

{ivoryos-1.2.0b1.dist-info → ivoryos-1.2.2.dist-info}/top_level.txt

@@ -1,2 +1 @@
 ivoryos
-tests

ivoryos/routes/auth/templates/login.html

@@ -1,25 +0,0 @@
-{% extends 'base.html' %}
-{% block title %}IvoryOS | Login{% endblock %}
-
-
-{% block body %}
-    <div class= "login">
-        <div class="bg-white rounded shadow-sm flex-fill">
-            <div class="p-4" style="align-items: center">
-                <h5>Log in</h5>
-                <form role="form" method='POST' name="login" action="{{ url_for('auth.login') }}">
-                    <div class="input-group mb-3">
-                        <label class="input-group-text" for="username">Username</label>
-                        <input class="form-control" type="text" id="username" name="username">
-                    </div>
-                    <div class="input-group mb-3">
-                        <label class="input-group-text" for="password">Password</label>
-                        <input class="form-control" type="password" id="password" name="password">
-                    </div>
-                    <button type="submit" class="btn btn-secondary" name="login" style="width: 100%;">login</button>
-                </form>
-                <p class="message">Not registered? <a href="{{ url_for('auth.signup') }}">Create a new account</a>
-            </div>
-        </div>
-    </div>
-{% endblock %}

ivoryos/routes/auth/templates/signup.html

@@ -1,32 +0,0 @@
-{% extends 'base.html' %}
-{% block title %}IvoryOS | Signup{% endblock %}
-
-
-{% block body %}
-<div class= "login">
-    <div class="bg-white rounded shadow-sm flex-fill">
-        <div class="p-4" style="align: center">
-            <h5>Create a new account</h5>
-            <form role="form" method='POST' name="signup" action="{{ url_for('auth.signup') }}">
-
-                <div class="input-group mb-3">
-                    <label class="input-group-text" for="username">Username</label>
-                    <input class="form-control" type="text" id="username" name="username" required>
-                </div>
-                <div class="input-group mb-3">
-                    <label class="input-group-text" for="password">Password</label>
-                    <input class="form-control" type="password" id="password" name="password" required>
-                </div>
-{#                <div class="input-group mb-3">#}
-{#                    <label class="input-group-text" for="confirm_password">Confirm Password</label>#}
-{#                    <input class="form-control" type="confirm_password" id="confirm_password" name="confirm_password">#}
-{#                </div>#}
-
-                <button type="submit" class="btn btn-secondary" name="login" style="width: 100%;">Sign up</button>
-            </form>
-            <p class="message" >Already registered? <a href="{{ url_for('auth.login') }}">Sign In</a></p>
-        </div>
-    </div>
-</div>
-
-{% endblock %}

ivoryos/routes/control/templates/controllers.html

@@ -1,166 +0,0 @@
-{% extends 'base.html' %}
-{% block title %}IvoryOS | Controllers {% endblock %}
-
-{% block body %}
-<div id="overlay" class="overlay">
-    <div>
-        <h3 id="overlay-text"></h3>
-        <div class="spinner-border" role="status"></div>
-    </div>
-</div>
-<div class="container-fluid">
-  <div class="row">
-    <!-- Sidebar: Instruments -->
-    <nav class="col-md-3 col-lg-2 d-md-block bg-light sidebar py-3" style="height: 100vh; overflow-y: auto; position: sticky; top: 0;">
-      <div class="sidebar-sticky">
-        <!-- Deck Instruments -->
-        <div class="mb-4">
-          <div class="list-group">
-            {% for inst in defined_variables %}
-              <a class="list-group-item list-group-item-action d-flex align-items-center {% if instrument == inst %}active bg-primary text-white border-0{% else %}bg-light{% endif %}"
-                 href="{{ url_for('control.deck_controllers') }}?instrument={{ inst }}"
-                 style="border-radius: 0.5rem; margin-bottom: 0.5rem; transition: background 0.2s;">
-                <span class="flex-grow-1">{{ inst | format_name }}</span>
-                {% if instrument == inst %}
-                  <span class="ms-auto">&gt;</span>
-                {% endif %}
-              </a>
-            {% endfor %}
-          </div>
-        </div>
-
-
-
-        <!-- Temp Instruments -->
-        {% if temp_variables %}
-          <div class="mb-4">
-            <h6 class="fw-bold text-secondary mb-2" style="letter-spacing: 1px;">Temp Instruments</h6>
-            <div class="list-group">
-              {% for inst in temp_variables %}
-                <a class="list-group-item list-group-item-action d-flex align-items-center {% if instrument == inst %}active bg-warning text-dark border-0{% else %}bg-light{% endif %}"
-                   href="{{ url_for('control.deck_controllers') }}?instrument={{ inst }}"
-                   style="border-radius: 0.5rem; margin-bottom: 0.5rem; transition: background 0.2s;">
-                  <span class="flex-grow-1">{{ inst | format_name }}</span>
-                  {% if instrument == inst %}
-                    <span class="ms-auto">&gt;</span>
-                  {% endif %}
-                </a>
-              {% endfor %}
-            </div>
-          </div>
-        {% endif %}
-        <!-- Action Buttons -->
-        <div class="mb-4">
-          <a href="{{ url_for('control.file.download_proxy', filetype='proxy') }}" class="btn btn-outline-primary w-100 mb-2">
-            Download proxy
-          </a>
-          <a href="{{ url_for('control.temp.new_controller') }}" class="btn btn-outline-success w-100">
-            New connection
-          </a>
-        </div>
-      </div>
-    </nav>
-
-    <!-- Main: Method Cards -->
-    <main class="col-md-9 ms-sm-auto col-lg-10 px-md-4" style="height: 100vh; overflow-y: auto;">
-      {% if instrument%}
-{#        <h2 class="text-secondary">{{ instrument }} controller</h2>#}
-        <div class="grid-container" id="sortable-grid" style="display: grid; grid-template-columns: repeat(auto-fit, minmax(350px, 1fr)); gap: 1rem; width: 100%;">
-          {% set hidden = session.get('hidden_functions', {}) %}
-          {% set hidden_instrument = hidden.get(instrument, []) %}
-          {% for function, form in forms.items() %}
-            {% if function not in hidden_instrument %}
-              <div class="card" id="{{function}}" style="margin: 0;">
-                <div class="bg-white rounded shadow-sm h-100">
-                  <i class="bi bi-info-circle ms-2" data-bs-toggle="tooltip" data-bs-placement="top" title='{{ form.hidden_name.description or "Docstring is not available" }}' ></i>
-                    <a href="{{ url_for('control.hide_function', instrument=instrument, function=function) }}"
-                       data-method="patch" data-payload='{"hidden":true}' class="toggle-visibility">
-                       <i style="float: right;" class="bi bi-eye-slash-fill text-muted" title="Hide function"></i>
-                    </a>
-                    <div class="form-control" style="border: none">
-                        <form role="form" method='POST' name="{{function}}" id="{{function}}" action="{{ url_for('control.deck_controllers') }}?instrument={{ instrument }}">
-                      <div class="form-group">
-                        {{ form.hidden_tag() }}
-                        {% for field in form %}
-                          {% if field.type not in ['CSRFTokenField', 'HiddenField'] %}
-                            <div class="input-group mb-3">
-                              <label class="input-group-text">{{ field.label.text | format_name }}</label>
-                              {% if field.type == "SubmitField" %}
-                                {{ field(class="btn btn-dark") }}
-                              {% elif field.type == "BooleanField" %}
-                                {{ field(class="form-check-input") }}
-                              {% else %}
-                                {{ field(class="form-control") }}
-                              {% endif %}
-                            </div>
-                          {% endif %}
-                        {% endfor %}
-                      </div>
-                      <div class="input-group mb-3">
-                        <button type="submit" name="{{ function }}" id="{{ function }}" class="form-control" style="background-color: #a5cece;">
-                            {{ function | format_name }}
-                        </button>
-                      </div>
-                    </form>
-                  </div>
-                </div>
-              </div>
-            {% endif %}
-          {% endfor %}
-        </div>
-        <!-- Hidden functions accordion -->
-        <div class="accordion accordion-flush" id="accordionActions" >
-          <div class="accordion-item">
-            <h4 class="accordion-header">
-              <button class="accordion-button collapsed" type="button" data-bs-toggle="collapse" data-bs-target="#hidden">
-                Hidden functions
-              </button>
-            </h4>
-          </div>
-          <div id="hidden" class="accordion-collapse collapse" data-bs-parent="#accordionActions">
-            <div class="accordion-body">
-              {% for function in hidden_instrument %}
-                <div>
-                  {{ function }}
-                    <a href="{{ url_for('control.hide_function', instrument=instrument, function=function) }}"
-                       data-method="patch" data-payload='{"hidden":false}' class="toggle-visibility">
-                       <i class="bi bi-eye-fill text-success" title="Show function"></i>
-                    </a>
-                </div>
-              {% endfor %}
-            </div>
-          </div>
-        </div>
-        <script>
-
-            document.querySelectorAll('.toggle-visibility').forEach(el => {
-              el.addEventListener('click', e => {
-                e.preventDefault();
-                const url = el.getAttribute('href');
-                const payload = JSON.parse(el.getAttribute('data-payload') || '{}');
-                fetch(url, {
-                  method: 'PATCH',
-                  headers: {
-                    'Content-Type': 'application/json'
-                  },
-                  body: JSON.stringify(payload)
-                }).then(response => {
-                  if (response.ok) {
-                    location.reload(); // or update the DOM directly
-                  }
-                });
-              });
-            });
-
-          const saveOrderUrl = `{{ url_for('control.save_order', instrument=instrument) }}`;
-          const buttonIds = {{ session['card_order'][instrument] | tojson }};
-        </script>
-        <script src="{{ url_for('static', filename='js/sortable_card.js') }}"></script>
-        <script src="{{ url_for('static', filename='js/overlay.js') }}"></script>
-      {% else %}
-        <div class="alert alert-info mt-4">Select an instrument to view its methods.</div>
-      {% endif %}
-    </main>
-  </div>
-</div>
-{% endblock %}

ivoryos/routes/control/templates/controllers_new.html

@@ -1,112 +0,0 @@
-{% extends 'base.html' %}
-     {% block title %}IvoryOS | New devices{% endblock %}
-
-     {% block body %}
-     <div class="row">
-         <!-- Available Python API -->
-         <div class="col-xl-4 col-lg-4 col-md-6 mb-4">
-             <div class="card shadow-sm mb-4">
-                 <div class="card-header">
-                     <h5 class="mb-0">Available Python API</h5>
-                 </div>
-                 <div class="card-body">
-                     {% for instrument in api_variables %}
-                         <div class="card mb-2">
-                             <div class="card-body p-2">
-                                 <a href="{{ url_for('control.temp.new_controller', instrument=instrument) }}" class="text-dark stretched-link">{{ instrument }}</a>
-                             </div>
-                         </div>
-                     {% endfor %}
-                     <div class="card mt-3">
-                         <div class="card-body p-2">
-                             <a data-bs-toggle="modal" href="#importAPI" class="stretched-link">
-                                 <i class="bi bi-folder-plus"></i> Import API
-                             </a>
-                         </div>
-                     </div>
-                 </div>
-             </div>
-         </div>
-
-         <!-- Connecting Device -->
-         <div class="col-xl-5 col-lg-5 col-md-6 mb-4">
-             {% if device %}
-{#                 {{ device }}#}
-             <div class="card shadow-sm mb-4">
-                 <div class="card-header">
-                     <h5 class="mb-0">Connecting</h5>
-                 </div>
-                 <div class="card-body">
-                     <form role="form" method="POST" name="init" action="{{ url_for('control.temp.new_controller', instrument=instrument) }}">
-                         <div class="mb-3">
-                             <label class="form-label" for="device_name">Name this device</label>
-                             <input class="form-control" type="text" id="device_name" name="device_name" aria-describedby="nameHelpBlock" placeholder="e.g. {{device.__name__}}_1">
-                             <div id="nameHelpBlock" class="form-text">
-                                 Name your instrument, avoid names that are defined on the right
-                             </div>
-                         </div>
-                         {% for arg in device.__init__.__annotations__ %}
-                             {% if not arg == "return" %}
-                                 <div class="mb-3">
-                                     <label class="form-label" for="{{arg}}">{{arg}}</label>
-                                     <input class="form-control" type="text" id="{{arg}}" name="{{arg}}"
-                                         placeholder="{{device.__init__.__annotations__[arg].__name__}}"
-                                         value="{{args.parameters[arg].default if not args.parameters[arg].default.__name__ == '_empty' else ''}}">
-                                     {% if device.__init__.__annotations__[arg].__module__ is not in ["builtins", "typing"] %}
-                                         <a role="button" href="{{ url_for('control.temp.new_controller', instrument=device.__init__.__annotations__[arg].__name__) }}" class="btn btn-secondary btn-sm mt-2">Initialize {{device.__init__.__annotations__[arg].__name__}} first</a>
-                                     {% endif %}
-                                 </div>
-                             {% endif %}
-                         {% endfor %}
-                         <button type="submit" class="btn btn-dark">Connect</button>
-                     </form>
-                 </div>
-             </div>
-             {% endif %}
-         </div>
-
-         <!-- Defined Instruments -->
-         <div class="col-xl-3 col-lg-3 col-md-6 mb-4">
-             <div class="card shadow-sm mb-4">
-                 <div class="card-header">
-                     <h5 class="mb-0">Defined Instruments</h5>
-                 </div>
-                 <div class="card-body">
-                     {% if defined_variables %}
-                         <ul class="list-group">
-                             {% for instrument in defined_variables %}
-                                 <li class="list-group-item">{{ instrument }}</li>
-                             {% endfor %}
-                         </ul>
-                     {% else %}
-                         <span class="text-muted">No instruments defined.</span>
-                     {% endif %}
-                 </div>
-             </div>
-         </div>
-     </div>
-
-     <!-- Import API Modal -->
-     <div class="modal fade" id="importAPI" tabindex="-1" aria-labelledby="importModal" aria-hidden="true">
-         <div class="modal-dialog">
-             <div class="modal-content">
-                 <div class="modal-header">
-                     <h1 class="modal-title fs-5" id="importModal">Import API by file path</h1>
-                     <button type="button" class="btn-close" data-bs-dismiss="modal" aria-label="Close"></button>
-                 </div>
-                 <form method="POST" action="{{ url_for('control.temp.import_api') }}" enctype="multipart/form-data">
-                     <div class="modal-body">
-                         <div class="mb-3">
-                             <label class="form-label" for="filepath">File Path:</label>
-                             <input type="text" class="form-control" name="filepath" id="filepath">
-                         </div>
-                     </div>
-                     <div class="modal-footer">
-                         <button type="button" class="btn btn-secondary" data-bs-dismiss="modal">Close</button>
-                         <button type="submit" class="btn btn-primary">Save</button>
-                     </div>
-                 </form>
-             </div>
-         </div>
-     </div>
-     {% endblock %}

ivoryos/routes/data/templates/components/step_card.html

@@ -1,13 +0,0 @@
-<div class="card mb-2 {{ 'border-danger text-danger bg-light' if step.run_error else 'border-secondary' }}">
-  <div class="card-body p-2">
-    <strong>{{ step.method_name | format_name }}</strong>
-    <small class="text-muted">
-      <i class="fas fa-play-circle me-1"></i> Start: {{ step.start_time.strftime('%H:%M:%S') if step.start_time else 'N/A' }}
-      <i class="fas fa-stop-circle ms-2 me-1"></i> End: {{ step.end_time.strftime('%H:%M:%S') if step.end_time else 'N/A' }}
-      <!-- {% if step.run_error %}
-        <i class="fas fa-stop-circle ms-2 me-1"></i> Error: {{ step.run_error if step.run_error else 'N/A' }}
-      {% endif %} -->
-    </small>
-    <!-- <small>Error: {{ step.run_error }}</small> -->
-  </div>
-</div>