Update environment for new location features

Snakefile

@@ -40,6 +40,7 @@ if config["BARNETT_LOCATION"]["COMPUTE"]:
     if config["BARNETT_LOCATION"]["LOCATIONS_TO_USE"] == "RESAMPLE_FUSED":
         if config["BARNETT_LOCATION"]["DB_TABLE"] in config["PHONE_VALID_SENSED_BINS"]["TABLES"]:
             files_to_compute.extend(expand("data/interim/{pid}/phone_sensed_bins.csv", pid=config["PIDS"]))
+            files_to_compute.extend(expand("data/raw/{pid}/{sensor}_resampled.csv", pid=config["PIDS"], sensor=config["BARNETT_LOCATION"]["DB_TABLE"]))
         else:
             raise ValueError("Error: Add your locations table (and as many sensor tables as you have) to [PHONE_VALID_SENSED_BINS][TABLES] in config.yaml. This is necessary to compute phone_sensed_bins (bins of time when the smartphone was sensing data) which is used to resample fused location data (RESAMPLED_FUSED)")            
     files_to_compute.extend(expand("data/raw/{pid}/{sensor}_raw.csv", pid=config["PIDS"], sensor=config["BARNETT_LOCATION"]["DB_TABLE"]))
@@ -119,6 +120,7 @@ if config["DORYAB_LOCATION"]["COMPUTE"]:
     if config["DORYAB_LOCATION"]["LOCATIONS_TO_USE"] == "RESAMPLE_FUSED":
         if config["DORYAB_LOCATION"]["DB_TABLE"] in config["PHONE_VALID_SENSED_BINS"]["TABLES"]:
             files_to_compute.extend(expand("data/interim/{pid}/phone_sensed_bins.csv", pid=config["PIDS"]))
+            files_to_compute.extend(expand("data/raw/{pid}/{sensor}_resampled.csv", pid=config["PIDS"], sensor=config["DORYAB_LOCATION"]["DB_TABLE"]))
         else:
             raise ValueError("Error: Add your locations table (and as many sensor tables as you have) to [PHONE_VALID_SENSED_BINS][TABLES] in config.yaml. This is necessary to compute phone_sensed_bins (bins of time when the smartphone was sensing data) which is used to resample fused location data (RESAMPLED_FUSED)")      
     files_to_compute.extend(expand("data/raw/{pid}/{sensor}_raw.csv", pid=config["PIDS"], sensor=config["DORYAB_LOCATION"]["DB_TABLE"]))

docs/develop/environments.rst

@@ -0,0 +1,18 @@
+Manage virtual environments
+====================
+
+**Add new packages**
+
+Try to install any new package using `conda install my_package`. If a package is not available in one of conda's channels you can install it with pip but make sure your virtual environment is active.
+
+**Update your conda environment.yaml**
+
+After installing a new package you can use the following command in your terminal to update your ``environment.yaml`` before publishing your pipeline. Note that we ignore the package version for ``libfortran`` to keep compatibility with Linux:
+
+    ``conda env export --no-builds | sed 's/^.*libgfortran.*$/  - libgfortran/' >  environment.yml``
+
+**Update and prune your conda environment from a environment.yaml file**
+
+Execute the following command in your terminal. See https://docs.conda.io/projects/conda/en/latest/user-guide/tasks/manage-environments.html#updating-an-environment
+
+    ``conda env update --prefix ./env --file environment.yml  --prune``

docs/index.rst

@@ -32,6 +32,7 @@ Contents:
 
    develop/documentation
    develop/features
+   develop/environments
    develop/contributors
    develop/testing
    develop/test_cases

environment.yml

@@ -1,24 +1,25 @@
-name: moshi-env
+name: rapids202007
 channels:
-  - anaconda
   - conda-forge
+  - anaconda
   - defaults
 dependencies:
   - appdirs=1.4.3
   - arrow=0.15.2
   - asn1crypto=1.2.0
+  - astropy=4.0.1.post1
   - attrs=19.3.0
   - binaryornot=0.4.4
   - blas=1.0
   - bzip2=1.0.8
-  - ca-certificates=2019.10.16
+  - ca-certificates=2020.6.24
-  - certifi=2019.9.11
+  - certifi=2020.6.20
   - cffi=1.13.1
   - chardet=3.0.4
   - click=7.0
   - cookiecutter=1.6.0
   - cryptography=2.7
-  - datrie=0.8
+  - datrie=0.8.2
   - docutils=0.15.2
   - future=0.18.1
   - gitdb2=2.0.6
@@ -28,10 +29,13 @@ dependencies:
   - intel-openmp=2019.4
   - jinja2=2.10.3
   - jinja2-time=0.2.0
+  - joblib=0.16.0
   - jsonschema=3.1.1
   - libcxx=9.0.0
+  - libedit=3.1.20181209
   - libffi=3.2.1
   - libgfortran
+  - llvm-openmp=10.0.0
   - markupsafe=1.1.1
   - mkl=2019.4
   - mkl-service=2.3.0
@@ -41,7 +45,7 @@ dependencies:
   - ncurses=6.1
   - numpy=1.17.2
   - numpy-base=1.17.2
-  - openssl=1.1.1
+  - openssl=1.1.1g
   - pandas=0.25.2
   - pbr=5.4.3
   - pip=19.3.1
@@ -58,6 +62,7 @@ dependencies:
   - readline=8.0
   - requests=2.22.0
   - retrying=1.3.3
+  - scikit-learn=0.22.1
   - scipy=1.3.1
   - setuptools=41.6.0
   - six=1.12.0
@@ -74,8 +79,14 @@ dependencies:
   - zlib=1.2.11
   - pip:
     - configargparse==0.15.1
+    - decorator==4.4.2
+    - ipython-genutils==0.2.0
+    - jupyter-core==4.6.3
+    - nbformat==5.0.7
     - pyrsistent==0.15.5
     - ratelimiter==1.2.0.post0
-    - snakemake==5.7.1
+    - snakemake==5.20.1
-prefix: /usr/local/Caskroom/miniconda/base/envs/moshi-env
+    - toposort==1.5
+    - traitlets==4.3.3
+prefix: /usr/local/Caskroom/miniconda/base/envs/rapids202007