Add example and introduce FlowchemDeviceClients

.github/workflows/codeql.yml

@@ -0,0 +1,37 @@
+name: "CodeQL"
+
+on:
+  push:
+    branches: [ "main" ]
+  pull_request:
+    branches: [ "main" ]
+  schedule:
+    - cron: '40 3 * * 2'
+
+jobs:
+  analyze:
+    name: Analyze
+    runs-on: 'ubuntu-latest'
+    timeout-minutes: 360
+    permissions:
+      actions: read
+      contents: read
+      security-events: write
+
+    strategy:
+      fail-fast: false
+
+    steps:
+    - name: Checkout repository
+      uses: actions/checkout@v3
+
+    # Initializes the CodeQL tools for scanning.
+    - name: Initialize CodeQL
+      uses: github/codeql-action/init@v2
+      with:
+        languages: 'python'
+
+    - name: Perform CodeQL Analysis
+      uses: github/codeql-action/analyze@v2
+      with:
+        category: "/language:python"

.github/workflows/publish_pypi.yml

@@ -28,14 +28,14 @@ jobs:
       - name: Publish distribution 📦 to Test PyPI
         uses: pypa/gh-action-pypi-publish@release/v1
         with:
-          repository_url: https://test.pypi.org/legacy/
-          skip_existing: true
+          repository-url: https://test.pypi.org/legacy/
+          skip-existing: true
 
       - name: Publish distribution 📦 to PyPI
         if: startsWith(github.ref_name, 'v')
         uses: pypa/gh-action-pypi-publish@release/v1
 
-  build-release-gh:
+  build-release-github:
     runs-on: ubuntu-latest
     steps:
       - uses: actions/checkout@master

.github/workflows/python-app.yml

@@ -15,6 +15,10 @@ jobs:
     timeout-minutes: 30
     strategy:
       matrix:
+        python-version: [
+          "3.11",
+          "3.12-dev",
+        ]
         operating-system:
           - ubuntu-latest
           - windows-latest
@@ -24,19 +28,19 @@ jobs:
       - name: Checkout
         uses: actions/checkout@v3
 
-      - name: Set up Python 3.11
+      - name: Set up Python
         uses: actions/setup-python@v4
         with:
-          python-version: '3.11'
+          python-version: ${{ matrix.python-version }}
 
       - name: Install flowchem
         run: |
-            python -m pip install .[dev,types,test]
+            python -m pip install .[ci]
             pip freeze
 
       - name: Run mypy
         run: |
-            mypy --check-untyped-defs --python-version 3.10 --ignore-missing-imports ./src
+            mypy --check-untyped-defs --python-version 3.11 --ignore-missing-imports ./src
 
       - name: Run ruff
         run: ruff .

.gitignore

@@ -129,3 +129,4 @@ dmypy.json
 .pyre/
 /flowchem/devices/Vapourtec/commands.py
 /src/flowchem/devices/knauer_hplc_nda.py
+.ruff_cache

.readthedocs.yml

@@ -7,7 +7,7 @@ version: 2
 build:
   os: ubuntu-20.04
   tools:
-    python: "3.10"
+    python: "3.11"
 
 sphinx:
    configuration: docs/conf.py

docs/add_device/add_to_flowchem.md

@@ -38,7 +38,7 @@ either directly or with an intermediate `/flowchem/devices/weasley/__init__.py`
 ### Device configuration
 Additional parameters needed for the device setup can be specified in the `__init__` method, if a default is provided
 the parameter will also be optional in the device section in the configuration file.
-In our case, the ExtentableEar has an optional length parameter, with a default value of "10 cm".
+In our case, the ExtendableEar has an optional length parameter, with a default value of "10 cm".
 To prevent ambiguities, all amounts with units should be provided as strings and parsed by the pint UnitRegistry
 `flowchem.ureg`.
 ```python
@@ -120,7 +120,7 @@ For example, we can define three methods: one to start the recording, one to sto
 The stop method will be responsible for returning the path of the file where the recording was saved.
 
 ```python
-from flowchem.components.sensors.base_sensor import Sensor
+from flowchem.components.sensors.sensor import Sensor
 
 
 class Microphone(Sensor):
@@ -155,31 +155,32 @@ commands to our device and some metadata about our device:
 ```python
 ...
 from flowchem.devices.weasley.extendable_ear_microphone import ExtendableEarMicrophone
-from flowchem.devices.flowchem_device import FlowchemDevice, DeviceInfo, Person
+from flowchem.devices.flowchem_device import FlowchemDevice
+from flowchem.components.device_info import DeviceInfo, Person
 
 
 class ExtendableEar(FlowchemDevice):
-    metadata = DeviceInfo(
-        authors=[Person(name="George Weasley", email="[email protected]"),
-                 Person(name="Fred Weasley", email="[email protected]")],
-        maintainers=[Person(name="George Weasley", email="[email protected]")],
-        manufacturer="Weasley & Weasley",
-        model="Extendable Ear",
-    )
+    def __init__(self, name):
+        super().__init__(name)
+        self.device_info.manufacturer = "Weasley & Weasley",
+        self.device_info.authors = [Person(name="George Weasley", email="[email protected]"),
+                     Person(name="Fred Weasley", email="[email protected]")]
+        self.device_info.model = "Extendable Ear"
 
     ...
 
     def send_command(self, command):
         print(command)  # This is in place of actual communication with the device
 
-   def components(self):
-        return ExtendableEarMicrophone("microphone", self),
+
+def components(self):
+    return ExtendableEarMicrophone("microphone", self),
 ```
 
 Now if we run `flowchem ear.toml` again the server will start successfully and show the metadata info together with the
 `start` and `stop` methods.
 
-![](../add_device/extendable_ear1.png)
+![](extendable_ear1.png)
 
 However, executing start and stop will not execute any code.
 For that we need to add some code in out `ExtendableEarMicrophone` to transform these calls into action.
@@ -202,7 +203,7 @@ class ExtendableEarMicrophone(Microphone):
 If we run `flowchem ear.toml` once again we can now see the code in `ExtendableEar` being executed when the API
 is called.
 
-![](../add_device/extendable_ear2.png)
+![](extendable_ear2.png)
 
 
 Finally, if we want to support some additional feature off our device that go beyond those of the standard component,

docs/api/elite11/api.md

@@ -1,4 +1,4 @@
-# Havard Apparatus Elite11
+# Harvard Apparatus Elite11
 See the [how-to guide](../../devices/pumps/elite11.md) to configure an Elite11 object.
 
 ```{eval-rst}

docs/api/icir/api.md

@@ -1,4 +1,4 @@
-# MattlerToledo iCIR
+# MettlerToledo iCIR
 
 See the [how-to guide](../../devices/analytics/icir.md) to configure an IcIR object.
 

docs/api/vici_valve/api.md

@@ -1,4 +1,4 @@
-# Vici Valco Unviersal Valve Actuator
+# Vici Valco Universal Valve Actuator
 See the [how-to guide](../../devices/valves/vici_valve.md) to configure a ViciValve object.
 
 ```{eval-rst}

docs/contribute.md

@@ -48,8 +48,8 @@ Moreover, the source code in the `flowchem` packages is organized in:
 
    * Create a branch for the feature you want to work on. Since the branch name will appear in the merge message, use a
      sensible name.
-     For example, if you intend to add support for a new device type, called ExtendibleEar a good candidate
-     could be ‘add-extendible-ear-support’: `git checkout -b add-extendible-ear-support`
+     For example, if you intend to add support for a new device type, called ExtendableEar a good candidate
+     could be ‘add-extendable-ear-support’: `git checkout -b add-extendible-ear-support`
 
    * Commit locally as you progress (`git add` and `git commit`).
      Use a properly formatted commit message, and ideally write tests that fail before your change and pass afterward.

docs/getting_started.md

@@ -11,7 +11,7 @@ In a typical scenario, flowchem:
 <img src="./_static/architecture_v1.svg" alt="Flowchem software architecture (devices/config/server)" class="bg-primary mb-1" width="100%">
 
 **Figure 1** Schematic representation of flowchem software architecture.
-An heterogeneous collection of devices is physically connected to a control PC.
+A heterogeneous collection of devices is physically connected to a control PC.
 The configuration file in TOML format specifies the connection parameters for each device.
 After running flowchem with that configuration, a web server is started to control each device via a single API.
 :::

docs/json2yml.py

@@ -5,5 +5,5 @@
 import yaml
 
 print(
-    yaml.dump(json.load(open(sys.argv[1])), default_flow_style=False, sort_keys=False)
+    yaml.dump(json.load(open(sys.argv[1])), default_flow_style=False, sort_keys=False),
 )

docs/learning/tutorial.md

@@ -1,7 +1,7 @@
 # Introductory tutorial
 
-Something something on how to write config
+Something on how to write config
 
-Something something on how to run server
+Something on how to run server
 
-Something something on how to consume the API
+Something on how to consume the API with the clients or OpenAPI things

examples/README.md

@@ -0,0 +1,3 @@
+# Examples
+
+This folder collects example of the use of flowchem devices.