Merge pull request #3 from TerrainBento/barnhark/pre_submission_changes

Barnhark/pre submission changes

.travis.yml

@@ -61,6 +61,6 @@ install:
 - pip install -e .
 script:
 - pip install pytest pytest-cov coveralls
-- pip install jupyter pandas plotnine holoviews terrainbento
+- pip install jupyter pandas plotnine holoviews terrainbento tqdm
 - pytest umami tests/ --doctest-modules --cov=umami --cov-report=xml:$(pwd)/coverage.xml -vvv
 after_success: coveralls

appveyor.yml

@@ -28,7 +28,7 @@ install:
   - cmd: set PYTHONUNBUFFERED=1
   - cmd: conda config --set always_yes yes
   - cmd: pip install pytest
-  - cmd: pip install jupyter pandas plotnine holoviews terrainbento
+  - cmd: pip install jupyter pandas plotnine holoviews terrainbento tqdm
   - cmd: conda info
   - cmd: conda list
 

binder/postBuild

@@ -1,9 +1,13 @@
 #!/bin/bash
 
-pip install jupyter
-pip install holoviews
-pip install pandas
-pip install plotnine>=0.6.0
-pip install terrainbento>=1.1
+conda config --add channels conda-forge
+conda config --set channel_priority strict
 
-pip install -e .
+conda install jupyter
+conda install holoviews
+conda install pandas
+conda install plotnine>=0.6.0
+conda install terrainbento>=1.10.1
+conda install tqdm
+
+python setup.py install

environment-dev.yml

@@ -12,10 +12,11 @@ dependencies:
    # for the package
    - scipy
    - numpy
-   - landlab>=1.10
+   - landlab>=1.10.1
    # for the notebooks
    - jupyter
    - holoviews
    - pandas
+   - tqdm
    - plotnine>=0.6.0
    - terrainbento>=1.1

notebooks/DiscretizedMisfit.ipynb

@@ -31,6 +31,7 @@
     "\n",
     "from io import StringIO\n",
     "from itertools import product\n",
+    "from tqdm import tqdm\n",
     "\n",
     "import numpy as np\n",
     "\n",
@@ -285,8 +286,8 @@
    "source": [
     "out = {}\n",
     "for i, (duration,\n",
-    "        water_erodibility) in enumerate(product(durations,\n",
-    "                                                water_erodibilitys)):\n",
+    "        water_erodibility) in enumerate(tqdm(product(durations,\n",
+    "                                                water_erodibilitys))):\n",
     "    lowering_rate = 100 / duration\n",
     "    test_params = StringIO(\n",
     "        spec_string.format(duration=duration,\n",
@@ -453,7 +454,7 @@
    "cell_type": "markdown",
    "metadata": {},
    "source": [
-    "You can see that the magnitude and \n",
+    "You can see that the misfit function has a similar shape in `water_erodibility`-`duration` space as the misfit functions from the [prior example notebook](ExampleApplication.ipynb). However, you can see that the specific location of the misfit surface minimum varies in its location in parameter space depending on which of the discretized residual categories is examined. \n",
     "\n",
     "# Next Steps\n",
     "Congratulations on finishing the four part series of introductory notebooks. The next steps are to use umami in your own application. "
@@ -476,7 +477,7 @@
    "name": "python",
    "nbconvert_exporter": "python",
    "pygments_lexer": "ipython3",
-   "version": "3.7.4"
+   "version": "3.7.3"
   }
  },
  "nbformat": 4,

notebooks/ExampleApplication.ipynb

@@ -30,6 +30,7 @@
     "\n",
     "from io import StringIO\n",
     "from itertools import product\n",
+    "from tqdm import tqdm\n",
     "\n",
     "import numpy as np\n",
     "\n",
@@ -285,8 +286,8 @@
    "source": [
     "out = {}\n",
     "for i, (duration,\n",
-    "        water_erodibility) in enumerate(product(durations,\n",
-    "                                                water_erodibilitys)):\n",
+    "        water_erodibility) in enumerate(tqdm(product(durations,\n",
+    "                                                water_erodibilitys))):\n",
     "    lowering_rate = 100 / duration\n",
     "    test_params = StringIO(\n",
     "        spec_string.format(duration=duration,\n",

setup.py

@@ -26,5 +26,5 @@
     long_description_content_type="text/markdown",
     zip_safe=False,
     packages=find_packages(),
-    install_requires=["scipy", "numpy", "landlab>=1.10"],
+    install_requires=["scipy", "numpy", "landlab>=1.10.1"],
 )