Remove pytable import from pedpy requirements (#221)

.github/workflows/ci.yml

@@ -129,7 +129,7 @@ jobs:
       - name: Install wheel
         shell: bash
         run: |
-          python3 -m pip install --upgrade pip jupyter nbconvert nbformat matplotlib h5py
+          python3 -m pip install --upgrade pip jupyter nbconvert nbformat matplotlib h5py tables
           python3 -m pip install dist/*whl
 
       - name: Test if install was successful

docs/requirements.txt

@@ -7,4 +7,5 @@ sphinx-notfound-page==0.8.3
 sphinx-favicon==1.0.1
 sphinx-book-theme==1.0.1
 sphinx-autoapi==2.1.1
-h5py==3.9.0
+h5py~=3.9.0
+tables~=3.8.0

notebooks/getting_started.ipynb

@@ -5,6 +5,10 @@
    "execution_count": null,
    "id": "ba3330b8828e94e2",
    "metadata": {
+    "ExecuteTime": {
+     "end_time": "2023-09-11T09:20:17.991484381Z",
+     "start_time": "2023-09-11T09:20:17.985395162Z"
+    },
     "collapsed": false,
     "tags": [
      "remove_input"
@@ -93,6 +97,10 @@
    "execution_count": null,
    "id": "190bcba420e16730",
    "metadata": {
+    "ExecuteTime": {
+     "end_time": "2023-09-11T09:20:40.405073444Z",
+     "start_time": "2023-09-11T09:20:37.866263207Z"
+    },
     "collapsed": false
    },
    "outputs": [],

notebooks/user_guide.ipynb

@@ -265,6 +265,9 @@
   },
   {
    "cell_type": "markdown",
+   "metadata": {
+    "collapsed": false
+   },
    "source": [
     "#### Loading from text trajectory files\n",
     "\n",
@@ -306,14 +309,14 @@
     "\n",
     "If your data is structured in a different way please take a look at the next section.\n",
     "Since the data we want to analyze is from the data archive, we can directly load the {class}`trajectory data<trajectory_data.TrajectoryData>` with *PedPy*:  "
-   ],
-   "metadata": {
-    "collapsed": false
-   }
+   ]
   },
   {
    "cell_type": "code",
    "execution_count": null,
+   "metadata": {
+    "collapsed": false
+   },
    "outputs": [],
    "source": [
     "from pedpy import load_trajectory, TrajectoryUnit\n",
@@ -323,56 +326,71 @@
     "    default_unit=TrajectoryUnit.METER,  # needs to be provided as it not defined in the file\n",
     "    # default_frame_rate=25., # can be ignored here as the frame rate is defined in the file\n",
     ")"
-   ],
-   "metadata": {
-    "collapsed": false
-   }
+   ]
   },
   {
    "cell_type": "markdown",
-   "source": [
-    "The loaded {class}`trajectory data<trajectory_data.TrajectoryData>` look like:"
-   ],
    "metadata": {
     "collapsed": false
-   }
+   },
+   "source": [
+    "The loaded {class}`trajectory data<trajectory_data.TrajectoryData>` look like:"
+   ]
   },
   {
    "cell_type": "code",
    "execution_count": null,
+   "metadata": {
+    "collapsed": false
+   },
    "outputs": [],
    "source": [
     "from pedpy import plot_trajectories\n",
     "import matplotlib.pyplot as plt\n",
     "\n",
     "plot_trajectories(traj=traj).set_aspect(\"equal\")\n",
     "plt.show()"
-   ],
-   "metadata": {
-    "collapsed": false
-   }
+   ]
   },
   {
    "cell_type": "markdown",
+   "metadata": {
+    "collapsed": false
+   },
    "source": [
     "#### Loading from hdf5 trajectory files\n",
     "\n",
-    "For some experiments the [Jülich Data Archive](https://ped.fz-juelich.de/da/doku.php) also provides [HDF5](https://www.google.com/search?client=firefox-b-d&q=hdf5) trajectory files, with a structure described [here](https://ped.fz-juelich.de/da/doku.php?id=info).\n",
+    "For some experiments the [Jülich Data Archive](https://ped.fz-juelich.de/da/doku.php) also provides [HDF5](www.hdfgroup.org/HDF5) trajectory files, with a structure described [here](https://ped.fz-juelich.de/da/doku.php?id=info).\n",
     "These data are from a different experiment, and are only used to demonstrate how to load HDF5 files, it can be downloaded {download}`here <demo-data/single_file/00_01a.h5>` For this to work you need to install the `h5py` package via:\n",
     "\n",
     "```\n",
     "pip install h5py\n",
     "```\n",
     "\n",
+    "Also Pandas needs [PyTables]() to load HDF5 files directly.\n",
+    "It can be installed via:\n",
+    "\n",
+    "```\n",
+    "pip install tables\n",
+    "```\n",
+    "\n",
+    "If you are using a Mac with an ARM processor, there is some extra work to do. \n",
+    "First you need to install the [HDF5 library](https://www.hdfgroup.org/solutions/hdf5/), if you have [Homebrew](https://brew.sh/) installed, you may use `brew install hdf5`.\n",
+    "Afterward, you can install PyTables with:\n",
+    "\n",
+    "```\n",
+    "pip install git+https://github.com/PyTables/PyTables\n",
+    "```\n",
+    "\n",
     "To make the data usable for *PedPy* use:"
-   ],
-   "metadata": {
-    "collapsed": false
-   }
+   ]
   },
   {
    "cell_type": "code",
    "execution_count": null,
+   "metadata": {
+    "collapsed": false
+   },
    "outputs": [],
    "source": [
     "from pedpy import TrajectoryData\n",
@@ -388,10 +406,7 @@
     "\n",
     "traj_h5 = TrajectoryData(data=df_trajectory, frame_rate=frame_rate)\n",
     "traj_h5"
-   ],
-   "metadata": {
-    "collapsed": false
-   }
+   ]
   },
   {
    "cell_type": "markdown",

requirements.txt

@@ -4,7 +4,6 @@ pandas~=2.0
 Shapely~=2.0
 scipy~=1.11
 matplotlib~=3.7
-tables~=3.8.0
 
 # testing
 pytest~=7.4

setup.py

@@ -42,6 +42,5 @@
         "Shapely~=2.0",
         "scipy~=1.11",
         "matplotlib~=3.7",
-        "tables~=3.8",
     ],
 )