Merge pull request #1 from Gepetto/devel

Devel

.dockerignore

@@ -0,0 +1 @@
+.venv

.github/workflows/gepetuto_test.yml

@@ -1,22 +1,14 @@
-# This workflow will install Python dependencies, run tests and lint with a single version of Python
-# For more information see: https://docs.github.com/en/actions/automating-builds-and-tests/building-and-testing-python
-
 name: check with gepetuto
 
 on: [push, pull_request]
 
 jobs:
   build:
-
     runs-on: ubuntu-latest
-
     steps:
-    - uses: actions/checkout@v3
-    - name: Set up Python 3.10
-      uses: actions/setup-python@v3
+    - uses: actions/checkout@v4
+    - uses: actions/setup-python@v3
       with:
-        python-version: "3.10"
-    - name: Install dependencies
-      run: pipx install poetry && poetry install
-    - name: check with gepetuto
-      run: poetry run gepetuto -vvca all
+        python-version: "3.11"
+    - run: pip install .
+    - run: gepetuto -vvca all

0-introduction_to_numerical_robotics.ipynb

@@ -433,7 +433,7 @@
    "name": "python",
    "nbconvert_exporter": "python",
    "pygments_lexer": "ipython3",
-   "version": "3.8.10"
+   "version": "3.11.6"
   }
  },
  "nbformat": 4,

1-forward_geom.ipynb

@@ -634,7 +634,7 @@
    "cell_type": "markdown",
    "metadata": {},
    "source": [
-    "From (Laitenberger, M., Raison, M., Périé, D., & Begon, M. (2015). Refinement of the upper limb joint kinematics and dynamics using a subject-specific closed-loop forearm model. Multibody System Dynamics, 33(4), 413-438)."
+    "From (Laitenberger, M., Raison, M., P\u00e9ri\u00e9, D., & Begon, M. (2015). Refinement of the upper limb joint kinematics and dynamics using a subject-specific closed-loop forearm model. Multibody System Dynamics, 33(4), 413-438)."
    ]
   },
   {
@@ -687,7 +687,7 @@
    "name": "python",
    "nbconvert_exporter": "python",
    "pygments_lexer": "ipython3",
-   "version": "3.8.10"
+   "version": "3.11.6"
   }
  },
  "nbformat": 4,

Dockerfile

@@ -1,14 +1,13 @@
-FROM python:3.10
+FROM python:3.11
 
 RUN useradd -m user
 USER user
 WORKDIR /home/user/tp
 ENV PATH /home/user/.local/bin:$PATH
 CMD jupyter lab --no-browser --ip='*'
 
-ADD --chown=user requirements.txt .
+ADD --chown=user . .
+RUN git remote set-url origin https://github.com/gepetto/supaero2024
 RUN --mount=type=cache,sharing=locked,uid=1000,gid=1000,target=/home/user/.cache \
     python -m pip install --user -U pip \
- && python -m pip install --user -r requirements.txt
-
-ADD --chown=user . .
+ && python -m pip install --user .

README.md

@@ -6,96 +6,90 @@ The notebooks are in Python and based on the software [Pinocchio](https://github
 
 ## Set up
 
-### Linux, Python 3, PyPI
+### Default setup
 
-On a Linux system with Python 3, you can get the dependencies directly with +[pip (see installation procedure and update below)](#installing-pip):
+This setup should work on Linux / MacOS / WSL2.
+
+You **must** use a [virtualenv](https://docs.python.org/3/library/venv.html) or a similar.
+
+For example on Debian/Ubuntu, you can get started with:
 ```bash
-python3 -m pip install -r requirements.txt
+sudo apt install python-is-python3 python3-pip python3-venv
 ```
 
+To create a virtual environment and activate it:
+```bash
+python -m venv .venv
+source .venv/bin/activate
+```
 
-NB: you should consider using a [virtualenv](https://docs.python.org/3/library/venv.html)
+**Once in your virtual environment**, install this package:
+```bash
+pip install -U pip
+pip install .
+```
 
-Once you have the dependencies, you can start the server with `jupyter notebook`
+After that, you can start the server with `jupyter notebook`
 
 ### Docker
 
-On other systems, use use the virtualization provided by +Docker. A Docker image is provided, and can be started with:
+If the default setup is not working for you, as a backup solution, a Docker image is provided, and can be started with:
 
 ```bash
-sudo docker run --rm -p 7000:7000 -p 7001:7001 -p 7002:7002 -p 7003:7003 -p 7004:7004 -p 8888:8888 -v data:/home/user/tp -it gepetto/supaero
+docker run --rm -p 7000:7000 -p 7001:7001 -p 7002:7002 -p 7003:7003 -p 7004:7004 -p 8888:8888 -v data:/home/user/tp -it gepetto/supaero2024
 ```
 
 On Linux host systems, you may simply start the Docker with:
 
 ```bash
-sudo docker run --rm --net host -v data:/home/user/tp -it gepetto/supaero
+docker run --rm --net host -v data:/home/user/tp -it gepetto/supaero
 ```
 
 In case of big update, you must update the docker:
 ```bash
-sudo docker pull gepetto/supaero
+docker pull gepetto/supaero2024
 ```
 
+## Use
+
 ### Update the notebooks
 
 If the repository changes (for example when new tutorials are pushes), you need to update your local
 version by "pulling" it from the repository.
-On a native installation, just go in the folder containing the tutorials and execute ```git pull```
+On a native installation, just go in the folder containing the tutorials and execute `git pull`
 
 With a docker, execute the following:
 ```bash
-sudo docker run --rm -v data:/home/user/tp -it gepetto/supaero  git remote set-url origin https://github.com/gepetto/supaero2024
-```
-Then
-```bash
-sudo docker run --rm -v data:/home/user/tp -it gepetto/supaero  git pull --rebase origin main
+docker run --rm -v data:/home/user/tp -it gepetto/supaero git pull --rebase origin main
 ```
 
-To avoid conflict when pulling a new version, you should better to your modifications in copy of the original files,
+To avoid conflict when pulling a new version, you should better do your modifications in copy of the original files,
 not directly in the original files itself.
 
 ## Side notes
 
-### Installing pip
-
-Pip is a tool for installing and managing Python packages. You can install it with
-
-```bash
-sudo apt install python3-pip
-```
-
-The default version of +pip installed by +apt is not up to date, so upgrade it with
-```bash
-python3 -m pip install --upgrade --user
-```
+### Installing docker
 
-In general, running +pip is likely to run an alias on +pip in /usr, so either run it through python3 as explained above, or make sure your path select the right pip executable in your ~/.local. The option --user is kind of optional for recent +pip version, but removing it should work with a warning.
+See [how to get Docker](https://docs.docker.com/get-docker/).
 
-### Installing docker
+## Docker as normal user
 
-On linux, install docker with +apt (or see https://docs.docker.com/engine/install/ubuntu/).
+To avoid the need to run `sudo docker`:
 
 ```bash
-sudo apt install docker.io
+sudo usermod -aG docker nmansard
+newgrp docker
 ```
-On other OS, see [how to get Docker](https://docs.docker.com/get-docker/).
-
-
-# Join me on \[Matrix\]
-
-[\[Matrix\]](https://matrix.org/) is a distributed chat system that will be used during the class. Consider [creating an account](https://app.element.io/#/register) and join [the classroom channel](https://matrix.to/#/#supaero-robotics-2024:laas.fr).
 
+## Join me on \[Matrix\]
 
-# Set up of the system ... for admin only
+[\[Matrix\]](https://matrix.org/) is a distributed chat system that will be used during the class. Consider [creating
+an account](https://app.element.io/#/register) and join [the classroom
+channel](https://matrix.to/#/#supaero-robotics-2024:laas.fr).
 
-## Compile the code snipets
+## Set up of the system ... for admin only
 
-run ```python utils/generate.py```. The directories to be generated are listed in plain code (line 54).
-This script take the tp*/*py and produces tp*/generated/* files following the "# %jupyter_snippet" /
-"# %end_jupyter_snippet"  hashtag in the code.
-
-## Build and push the docker
+### Build and push the docker
 
 Build the docker as specified in Dockerfile. You need the buildkit for that. The following file +/etc/docker/deamon_json+ should contain:
 ```json
@@ -108,7 +102,7 @@ export DOCKER_BUILDKIT=1
 ```
 Then build:
 ```bash
-docker build . -t gepetto/supaero
+docker build -t gepetto/supaero2024 .
 ```
 Log to Docker-hub using your credentials.
 ```bash
@@ -117,12 +111,5 @@ docker login
 Use the login corresponding to +https://hub.docker.com/+.
 And push it to the Gepetto repository of Docker-hub.
 ```bash
-docker build -t gepetto/supaero
-```
-
-## Docker as normal user
-
-```bash
-sudo usermod -aG docker nmansard
-newgrp docker
+docker push gepetto/supaero2024
 ```

next/2-inv_geom.ipynb

@@ -194,7 +194,7 @@
    "metadata": {},
    "outputs": [],
    "source": [
-    "from supaero2023.meshcat_viewer_wrapper import MeshcatVisualizer, colors  # noqa: E402\n",
+    "from supaero2024.meshcat_viewer_wrapper import MeshcatVisualizer, colors  # noqa: E402\n",
     "\n",
     "viz = MeshcatVisualizer(robot)"
    ]
@@ -702,7 +702,7 @@
    "metadata": {},
    "outputs": [],
    "source": [
-    "from supaero2023. load_ur5_parallel import load_ur5_parallel  # noqa: E402\n",
+    "from supaero2024. load_ur5_parallel import load_ur5_parallel  # noqa: E402\n",
     "\n",
     "robot = load_ur5_parallel()"
    ]

next/3-invkine.ipynb

@@ -38,7 +38,7 @@
     "from numpy.linalg import pinv,inv,norm,svd,eig\n",
     "from tp3.tiago_loader import loadTiago\n",
     "import matplotlib.pylab as plt\n",
-    "from supaero2023.meshcat_viewer_wrapper import MeshcatVisualizer\n",
+    "from supaero2024.meshcat_viewer_wrapper import MeshcatVisualizer\n",
     "import unittest\n"
    ]
   },

next/4-dynamics.ipynb

@@ -40,7 +40,7 @@
     "import matplotlib.pylab as plt\n",
     "import quadprog\n",
     "from tp4.robot_hand import RobotHand\n",
-    "from supaero2023.meshcat_viewer_wrapper import MeshcatVisualizer"
+    "from supaero2024.meshcat_viewer_wrapper import MeshcatVisualizer"
    ]
   },
   {

next/5-2_controlopt.ipynb

@@ -107,7 +107,7 @@
    "source": [
     "# %load tp5/generated/arm_example_viz\n",
     "# Configure viewer\n",
-    "from supaero2023.meshcat_viewer_wrapper import MeshcatVisualizer\n",
+    "from supaero2024.meshcat_viewer_wrapper import MeshcatVisualizer\n",
     "viz = MeshcatVisualizer(robot)\n",
     "viz.display(robot_model.q0)\n",
     "viz.addBox('world/box',[.1,.1,.1], [1.,0,0,1])\n",

next/tp2/generated/parallel_robots_0

@@ -1,5 +1,5 @@
-from supaero2023.load_ur5_parallel import load_ur5_parallel
-from supaero2023.meshcat_viewer_wrapper import MeshcatVisualizer
+from supaero2024.load_ur5_parallel import load_ur5_parallel
+from supaero2024.meshcat_viewer_wrapper import MeshcatVisualizer
 
 # Load 4 Ur5 robots, placed at 0.3m from origin in the 4 directions x,y,-x,-y.
 robot = load_ur5_parallel()

next/tp3/control_head.py

@@ -12,9 +12,9 @@
 import numpy as np
 import pinocchio as pin
 from numpy.linalg import norm, pinv
+from tp3.tiago_loader import loadTiago
 
 from supaero2024.meshcat_viewer_wrapper import MeshcatVisualizer
-from tp3.tiago_loader import loadTiago
 
 plt.ion()
 

next/tp3/generated/inverse_kinematics_import

@@ -2,4 +2,4 @@ import pinocchio as pin
 from numpy.linalg import norm, pinv
 
 from tp3.tiago_loader import loadTiago
-from supaero2023.meshcat_viewer_wrapper import MeshcatVisualizer
+from supaero2024.meshcat_viewer_wrapper import MeshcatVisualizer

next/tp3/inverse_kinematics.py

@@ -14,9 +14,9 @@
 # %jupyter_snippet import
 import pinocchio as pin
 from numpy.linalg import norm, pinv
+from tp3.tiago_loader import loadTiago
 
 from supaero2024.meshcat_viewer_wrapper import MeshcatVisualizer
-from tp3.tiago_loader import loadTiago
 
 # %end_jupyter_snippet
 

next/tp4/collision_wrapper.py

@@ -1,8 +1,8 @@
 import numpy as np
 import pinocchio as pin
+from tp4.robot_hand import RobotHand
 
 from supaero2024.meshcat_viewer_wrapper import MeshcatVisualizer
-from tp4.robot_hand import RobotHand
 
 
 class CollisionWrapper:

next/tp4/solution_pd.py

@@ -5,9 +5,9 @@
 import numpy as np
 import pinocchio as pin
 from numpy.linalg import inv, norm
+from tp4.robot_hand import RobotHand
 
 from supaero2024.meshcat_viewer_wrapper import MeshcatVisualizer
-from tp4.robot_hand import RobotHand
 
 plt.ion()
 

next/tp5/generated/arm_example_viz

@@ -1,4 +1,4 @@
-from supaero2023.meshcat_viewer_wrapper import MeshcatVisualizer  # noqa E402
+from supaero2024.meshcat_viewer_wrapper import MeshcatVisualizer  # noqa E402
 
 viz = MeshcatVisualizer(robot)
 viz.display(robot_model.q0)