Major improvements to advanced tutorial (#13)

* Split advanced tutorial into 4 notebooks

also add a lot more discussion

* forgot to add notebook 5!

* repatch

* try to add advanced tutorials to testing

* add CLI run scripts

* Add support for Py>=3.8 in advanced example

* 250 -> 300 in notebook 7 (should pass more often)

* shift interfaces

* shift interfaces (regularly passes locally)

* fix syntax error

* shift interfaces

* shift interfaces again

* add comment about overlap error

Author: dwhswenson

.github/workflows/ci.yml

@@ -15,9 +15,9 @@ defaults:
     shell: bash -l {0}
 
 jobs:
-  tests:
+  intro-tutorial:
     runs-on: ubuntu-latest
-    name: "Test answer key"
+    name: "Intro tutorial"
     strategy:
       matrix:
         CONDA_PY:
@@ -34,6 +34,7 @@ jobs:
           python-version: ${{ matrix.CONDA_PY }}
           environment-file: binder/environment.yml
           activate-environment: ops-tutorial
+          miniforge-variant: Mambaforge
       - name: "Install testing tools"
         run: python -m pip install pytest nbval
       - name: "Conda info"
@@ -51,3 +52,42 @@ jobs:
             2_tps_analysis_tutorial.ipynb \
             3_committor_analysis_tutorial.ipynb \
             4_mstis_sampling_tutorial.ipynb
+
+  advanced-tutorial:
+    runs-on: ubuntu-latest
+    name: "Advanced tutorial"
+    strategy:
+      matrix:
+        CONDA_PY:
+          - 3.7
+          - 3.8
+          - 3.9
+
+    steps:
+      - uses: actions/checkout@v2
+      - uses: actions/setup-python@v2
+      - uses: conda-incubator/setup-miniconda@v2
+        with:
+          auto-update-conda: true
+          python-version: ${{ matrix.CONDA_PY }}
+          environment-file: binder/environment.yml
+          activate-environment: ops-tutorial
+          miniforge-variant: Mambaforge
+      - name: "Install testing tools"
+        run: python -m pip install pytest nbval
+      - name: "Conda info"
+        run: |
+          conda info
+          conda list
+      - name: "Patch answers"
+        run: source devtools/patch-all
+      - name: "Run tests"
+        run: |
+          pytest --nbval-lax 5_custom_shooting_setup.ipynb
+          source devtools/run5.sh
+          pytest --nbval-lax \
+            6_custom_shooting_analysis.ipynb \
+            7_parallel_tis_setup.ipynb
+          source devtools/run7.sh
+          pytest --nbval-lax 8_parallel_tis_analysis.ipynb
+

1_tps_sampling_tutorial.ipynb

@@ -326,7 +326,9 @@
    "source": [
     "## Running the simulation\n",
     "\n",
-    "Now all the parts are in place, and we can run the simulation! First, we open a file to store the results in, and then we build the simulation and run it."
+    "Now all the parts are in place, and we can run the simulation! First, we open a file to store everything in, and then we build the simulation and run it.\n",
+    "\n",
+    "In practice, for a long-running simulation you might save all the relevant information to a \"setup\" file, and then use the OPS Command Line Interface (CLI) to run it (perhaps on a remote computer). The advantage of that approach is that you can re-use the same exact objects, guaranteeing that they will behave the same way and making analysis easier. That approach is described in notebook 5 of this tutorial. In this notebook, we'll directly run the simulation."
    ]
   },
   {
@@ -398,7 +400,7 @@
    "name": "python",
    "nbconvert_exporter": "python",
    "pygments_lexer": "ipython3",
-   "version": "3.7.3"
+   "version": "3.7.10"
   },
   "toc": {
    "base_numbering": 1,