Try to test on_topic notebooks as well (#13)

* update notebooks

* remove metadata from cells during tests

* update content and contextily installation

* add descartes

* typo

* update installation manual

* update gitignore

* move groundwater model directory

* update gitignore

* restructure and update practical examples

* last update for now

* add cbs_data analyse

* update twitter analysis

* reinstate some files to be ignored

* remove error in camel_bananas function

* update camel problem

* modify text

* remove notebook metadata as well (and not only cell metadata)

* minor changes

* remove all metadata from notebooks

* add on-topic to test

* update travis requirements

* fix travis test errors

* add pyproj to travis req

* add proj to travis req

* add proj4 to travis req

* remove proj from req

* another attempt to let travis install cartopy

* another attempt to let travis install cartopy

* another attempt to let travis install cartopy

* another attempt to let travis install cartopy

* another attempt to let travis install cartopy

* another attempt to let travis install cartopy

* another attempt to let travis install cartopy

* another attempt to let travis install cartopy

* another attempt to let travis install cartopy

* another attempt to let travis install cartopy

* another day another attempt:

* another day another attempt:

* another day another attempt:

* another day another attempt:

* add dependencies

* add dependency

* remove first folium notebook from tests because mplleaflet is not maintained anymore, see this issue plotly/plotly.py#2913

.travis.yml

@@ -4,17 +4,41 @@ language: python
 os:
   - linux
 
+env:
+    matrix:
+        - ENV_NAME="test-environment"
+          PYTHON_VERSION=3.7
+          PACKAGES="ipython>=7.0.0 numpy scipy matplotlib pandas jupyter cython proj4=5.2.0"
+
 branches:
   only:
     - master
 
 jobs:
   include:
-    - python: 3.7
-      dist: xenial
+    - dist: xenial
 
 # Install dependencies
 install:
+  # Install miniconda
+  # -----------------
+  - wget https://repo.continuum.io/miniconda/Miniconda3-latest-Linux-x86_64.sh -O miniconda.sh;
+  - bash miniconda.sh -b -p $HOME/miniconda
+  - export PATH="$HOME/miniconda/bin:$PATH"
+
+
+  # Create the basic testing environment
+  # ------------------------------------
+  - conda config --set always_yes yes
+  - conda config --add channels conda-forge
+
+  # Customise the testing environment
+  # ---------------------------------
+  - conda create -n $ENV_NAME python=$PYTHON_VERSION $PACKAGES
+  - source activate $ENV_NAME 
+
+  # Install packages
+  # ----------------
   - pip install -r requirements.travis.txt
   - pip install --upgrade pip
   - pip install codecov
@@ -25,6 +49,6 @@ install:
 # command to run tests
 script:
   - py.test ./autotest/test_01_basic.py -n 3
-
+  - py.test ./autotest/test_02_on_topic.py -n 3
 after_success:
   - python-codacy-coverage -r coverage.xml

Exercise_notebooks/Basic/basic1_use_jupyter/sources/Notebook Basics.ipynb

@@ -230,11 +230,7 @@
    ]
   }
  ],
- "metadata": {
-  "language_info": {
-   "name": "python"
-  }
- },
+ "metadata": {},
  "nbformat": 4,
  "nbformat_minor": 1
 }

Exercise_notebooks/On_topic/08_GIS/Geopandas.ipynb

@@ -199,7 +199,7 @@
    "metadata": {},
    "outputs": [],
    "source": [
-    "df_turbines = pd.read_excel(r'data\\turbines_ohvs.xlsx')\n",
+    "df_turbines = pd.read_excel(r'data/turbines_ohvs.xlsx')\n",
     "df_turbines.head()"
    ]
   },
@@ -481,7 +481,7 @@
    "metadata": {},
    "outputs": [],
    "source": [
-    "gdf_nybb = gpd.read_file(r'data\\nybb.shp')\n",
+    "gdf_nybb = gpd.read_file(r'data/nybb.shp')\n",
     "gdf_nybb.head()"
    ]
   },
@@ -531,7 +531,7 @@
    "metadata": {},
    "outputs": [],
    "source": [
-    "df_verkeer = pd.read_csv(r'data\\traffic_intensity_Utrecht.csv')\n",
+    "df_verkeer = pd.read_csv(r'data/traffic_intensity_Utrecht.csv')\n",
     "geometry = gpd.points_from_xy(df_verkeer['longitude'], df_verkeer['latitude'])\n",
     "gdf_verkeer = gpd.GeoDataFrame(df_verkeer.copy(), geometry=geometry)\n",
     "gdf_verkeer.head()"

Exercise_notebooks/On_topic/09_Code_Quality/03_Quality_ZEN_of_Python.ipynb

@@ -1204,7 +1204,16 @@
  ],
  "metadata": {
   "language_info": {
-   "name": "python"
+   "codemirror_mode": {
+    "name": "ipython",
+    "version": 3
+   },
+   "file_extension": ".py",
+   "mimetype": "text/x-python",
+   "name": "python",
+   "nbconvert_exporter": "python",
+   "pygments_lexer": "ipython3",
+   "version": "3.7.6"
   }
  },
  "nbformat": 4,

Exercise_notebooks/On_topic/24_pastas/3_stressmodels.ipynb

@@ -611,7 +611,7 @@
    "outputs": [],
    "source": [
     "ini_param = ml.parameters['initial'].values\n",
-    "sim_ini_param = ml.simulate(parameters=ini_param)\n",
+    "sim_ini_param = ml.simulate(p=ini_param)\n",
     "\n",
     "#visualise results\n",
     "sim_ini_param.plot(label='model simulation initial parameters')\n",
@@ -654,7 +654,7 @@
    "source": [
     "# simulate groundwater head with optimized parameters\n",
     "opt_param = ml.parameters['optimal'].values\n",
-    "sim_opt_param = ml.simulate(parameters=opt_param)\n",
+    "sim_opt_param = ml.simulate(p=opt_param)\n",
     "\n",
     "# or simply use\n",
     "sim_opt_param = ml.simulate()\n",
@@ -688,8 +688,8 @@
     "semi_opt_param[3] = 1.0\n",
     "\n",
     "\n",
-    "sim_opt_param = ml.simulate(parameters=opt_param)\n",
-    "sim_semi_opt = ml.simulate(parameters=semi_opt_param)\n",
+    "sim_opt_param = ml.simulate(p=opt_param)\n",
+    "sim_semi_opt = ml.simulate(p=semi_opt_param)\n",
     "\n",
     "#visualise results\n",
     "sim_opt_param.plot(label='model simulation optimal parameters')\n",

Exercise_notebooks/On_topic/24_pastas/4_pastas_project.ipynb

@@ -55,7 +55,7 @@
    "outputs": [],
    "source": [
     "# add the observations in all the files in the data-directory that end with _1.csv\n",
-    "datapath = r'data\\nb4'\n",
+    "datapath = r'data/nb4'\n",
     "files = [x for x in os.listdir(datapath) if x.endswith('_1.csv')]\n",
     "for file in files:\n",
     "    fname = os.path.join(datapath,file)\n",
@@ -71,7 +71,7 @@
    "metadata": {},
    "source": [
     "#### Exercise 1 <a name=\"ex1\"></a>\n",
-    "Create a pastas project. Add the observations in the `data\\nb4\\ex1`  to the model. Which measurements series has the lowest filter?"
+    "Create a pastas project. Add the observations in the `data/nb4/ex1` directory to the model. Which measurements series has the lowest filter?"
    ]
   },
   {
@@ -430,7 +430,7 @@
     "pr_q = ps.Project(name='exercise1')\n",
     "\n",
     "# add the observations in all the files in the data-directory that end with _1.csv\n",
-    "datapath_ex1 = r'data\\nb4\\ex1'\n",
+    "datapath_ex1 = r'data/nb4/ex1'\n",
     "files = [x for x in os.listdir(datapath_ex1) if x.endswith('_1.csv')]\n",
     "for file in files:\n",
     "    fname = os.path.join(datapath_ex1,file)\n",

autotest/test_02_on_topic.py

@@ -791,22 +791,6 @@ def test_11___Running_Bokeh_Applications():
     assert out == 0
     return 1
 
-def test_Folium01_and_mplleaflet():
-    fpath_rel = ['20_folium', 'Folium01_and_mplleaflet.ipynb']
-    subdir = fpath_rel[:-1]
-    fname = fpath_rel[-1]
-    fdir = os.path.join(*nb_dir, *subdir)
-    cwd = os.getcwd()
-    os.chdir(fdir)
-    try:
-        out = tf.run_notebook(fname, clearoutput=True)
-        os.chdir(cwd)
-    except Exception as e:
-        os.chdir(cwd)
-        raise(e)
-    assert out == 0
-    return 1
-
 def test_Folium02_CheckZorder():
     fpath_rel = ['20_folium', 'Folium02_CheckZorder.ipynb']
     subdir = fpath_rel[:-1]

requirements.travis.txt

@@ -1,8 +1,3 @@
-numpy>=1.15
-scipy>=1.2
-matplotlib>=3.0
-pandas>=0.24
-jupyter>=1.0.0
 lxml
 requests
 zeep
@@ -15,4 +10,14 @@ branca
 folium
 bokeh
 pastas
-nbformat
+xlrd
+sqlalchemy
+rasterio
+cartopy
+descartes
+mplleaflet
+contextily
+geographiclib
+networkx
+gpxpy
+pyshp