Fix Binder (release/4/dev) (#235)

* Update requirements.txt (add simphony-osp-simlammps)

* Use .binder directory

* Use custom docker image for Binder

* Fix minor issues in some notebooks

.binder/Dockerfile

@@ -0,0 +1,63 @@
+FROM debian:bullseye-slim
+
+
+ENV DEBIAN_FRONTEND=noninteractive
+
+
+# Install required packages: Jupyter and packages required to run notebooks.
+RUN apt-get -qq update && \
+    apt-get install --yes --no-install-recommends \
+    wget \
+    python3 python3-pip \
+    ipython3 python3-ipykernel \
+    jupyter jupyter-notebook jupyter-nbconvert  \
+    python3-jupyterlab-server \
+    python3-lammps \
+    graphviz ffmpeg && \
+    apt-get -qq purge && \
+    apt-get -qq clean && \
+    rm -rf /var/lib/apt/lists/*
+
+# Hardlink liblammps
+RUN ln /usr/lib/x86_64-linux-gnu/liblammps.so.0 /usr/lib/python3/dist-packages/lammps/liblammps.so
+
+# create user with a home directory
+ARG NB_USER
+ARG NB_UID
+ENV USER ${NB_USER}
+ENV HOME /home/${NB_USER}
+
+RUN adduser --disabled-password \
+    --gecos "Default user" \
+    --uid ${NB_UID} \
+    ${NB_USER}
+WORKDIR ${HOME}
+
+# Make sure the contents of our repo are in ${HOME}
+COPY . ${HOME}
+RUN chown -R ${NB_UID} ${HOME}
+USER ${NB_USER}
+
+# Add ~/.local/bin to PATH
+ENV PATH="${HOME}/.local/bin:${PATH}"
+
+
+# Update nbconvert
+RUN pip install --no-cache-dir nbconvert==6.4.3
+
+# Install requirements
+RUN pip install --no-cache-dir -r requirements.txt
+
+# Install multiprocess
+RUN pip install multiprocess
+
+# Install simlammps ontology
+RUN wget https://raw.githubusercontent.com/simphony/simlammps/main/simphony_osp_simlammps/simlammps.ttl
+RUN wget https://raw.githubusercontent.com/simphony/simlammps/main/simphony_osp_simlammps/simlammps.yml
+RUN pico install simlammps.yml
+
+# Install city and emmo ontologies
+RUN pico install city emmo
+
+# Fix problem with lammps not priting output to Python variables
+ENV PYTHONUNBUFFERED=1

docs/introduction/quickstart.ipynb

@@ -84,7 +84,14 @@
    "metadata": {},
    "outputs": [],
    "source": [
-    "#!pico install /path/to/simlammps"
+    "# if you are running the tutorial online using Binder, then the simlammps\n",
+    "# ontology is already pre-installed\n",
+    "\n",
+    "# otherwise, download `simlammps.ttl` and `simlammps.yml` from \n",
+    "# https://github.com/simphony/simlammps/tree/v4.0.0/simphony_osp_simlammps\n",
+    "# and run\n",
+    "\n",
+    "#!pico install simlammps.yml"
    ]
   },
   {
@@ -425,15 +432,16 @@
     }
    ],
    "source": [
-    "from simphony_osp.wrappers import SimLammps\n",
+    "from simphony_osp.wrappers import SimLAMMPS\n",
     "\n",
     "# open the SQLite database and create a new SimLAMMPS session\n",
     "sqlite_session = SQLite('atoms.db', create=False)\n",
-    "simlammps_session = SimLammps()\n",
+    "simlammps_session = SimLAMMPS()\n",
     "\n",
     "# prevent closing the sessions when leaving the contexts after \n",
     "# using the `with` statement\n",
-    "sqlite_session.locked = True, simlammps_session.locked = True\n",
+    "sqlite_session.locked = True\n",
+    "simlammps_session.locked = True\n",
     "\n",
     "# copy the individuals from the SQLite session to the SimLAMMPS session\n",
     "ontology_individuals_from_database = list(sqlite_session)\n",
@@ -582,7 +590,7 @@
  ],
  "metadata": {
   "kernelspec": {
-   "display_name": "Python 3",
+   "display_name": "Python 3 (ipykernel)",
    "language": "python",
    "name": "python3"
   },
@@ -596,7 +604,7 @@
    "name": "python",
    "nbconvert_exporter": "python",
    "pygments_lexer": "ipython3",
-   "version": "3.8.12"
+   "version": "3.10.7"
   }
  },
  "nbformat": 4,

docs/usage/sessions/introduction.ipynb

@@ -153,7 +153,9 @@
    "source": [
     "session_B = Session()\n",
     "\n",
-    "session_A.locked = True, session_B.locked = True  # this will be explained later\n",
+    "# this will be explained later\n",
+    "session_A.locked = True\n",
+    "session_B.locked = True\n",
     "\n",
     "with session_B:\n",
     "    london = city.City(name=\"London\", coordinates=[51.50737, -0.12767])\n",
@@ -190,7 +192,7 @@
  ],
  "metadata": {
   "kernelspec": {
-   "display_name": "Python 3",
+   "display_name": "Python 3 (ipykernel)",
    "language": "python",
    "name": "python3"
   },
@@ -204,7 +206,7 @@
    "name": "python",
    "nbconvert_exporter": "python",
    "pygments_lexer": "ipython3",
-   "version": "3.8.12"
+   "version": "3.10.7"
   },
   "toc-showcode": false,
   "toc-showtags": true

docs/usage/sessions/sparql.ipynb

@@ -249,18 +249,11 @@
     "    \n",
     "</div>"
    ]
-  },
-  {
-   "cell_type": "code",
-   "execution_count": null,
-   "metadata": {},
-   "outputs": [],
-   "source": []
   }
  ],
  "metadata": {
   "kernelspec": {
-   "display_name": "Python 3",
+   "display_name": "Python 3 (ipykernel)",
    "language": "python",
    "name": "python3"
   },
@@ -274,7 +267,7 @@
    "name": "python",
    "nbconvert_exporter": "python",
    "pygments_lexer": "ipython3",
-   "version": "3.8.12"
+   "version": "3.10.7"
   },
   "toc-showcode": false,
   "toc-showtags": true

requirements.txt

@@ -1,4 +1,5 @@
 simphony-osp == 4.0.0rc3
+simphony-osp-simlammps >= 4.0.0, < 5.0.0rc0
 jinja2 >= 3.0.3, < 4
 jupyter >= 1.0.0, < 2
 markupsafe >= 2.1.1, < 3