Merge pull request #482 from cmu-delphi/update-readmes

Update READMEs with make commands

Author: krivard

_template_python/README.md

@@ -7,15 +7,15 @@
 The indicator is run by directly executing the Python module contained in this
 directory. The safest way to do this is to create a virtual environment,
 installed the common DELPHI tools, and then install the module and its
-dependencies. To do this, run the following code from this directory:
+dependencies. To do this, run the following command from this directory:
 
 ```
-python -m venv env
-source env/bin/activate
-pip install ../_delphi_utils_python/.
-pip install .
+make install
 ```
 
+This command will install the package in editable mode, so you can make changes that
+will automatically propagate to the installed package. 
+
 All of the user-changable parameters are stored in `params.json`. To execute
 the module and produce the output datasets (by default, in `receiving`), run
 the following:
@@ -24,34 +24,39 @@ the following:
 env/bin/python -m delphi_NAME
 ```
 
-Once you are finished with the code, you can deactivate the virtual environment
-and (optionally) remove the environment itself.
+If you want to enter the virtual environment in your shell, 
+you can run `source env/bin/activate`. Run `deactivate` to leave the virtual environment. 
+
+Once you are finished, you can remove the virtual environment and 
+params file with the following:
 
 ```
-deactivate
-rm -r env
+make clean
 ```
 
 ## Testing the code
 
-To do a static test of the code style, it is recommended to run **pylint** on
-the module. To do this, run the following from the main module directory:
+To run static tests of the code style, run the following command:
 
 ```
-env/bin/pylint delphi_NAME
+make lint
 ```
 
-The most aggressive checks are turned off; only relatively important issues
-should be raised and they should be manually checked (or better, fixed).
-
 Unit tests are also included in the module. To execute these, run the following
 command from this directory:
 
 ```
-(cd tests && ../env/bin/pytest --cov=delphi_NAME --cov-report=term-missing)
+make test
+```
+
+To run individual tests, run the following:
+
+```
+(cd tests && ../env/bin/pytest <your_test>.py --cov=delphi_NAME --cov-report=term-missing)
 ```
 
 The output will show the number of unit tests that passed and failed, along
-with the percentage of code covered by the tests. None of the tests should
-fail and the code lines that are not covered by unit tests should be small and
-should not include critical sub-routines.
+with the percentage of code covered by the tests. 
+
+None of the linting or unit tests should fail, and the code lines that are not covered by unit tests should be small and
+should not include critical sub-routines. 

cdc_covidnet/README.md

@@ -10,12 +10,12 @@ installed the common DELPHI tools, and then install the module and its
 dependencies. To do this, run the following code from this directory:
 
 ```
-python -m venv env
-source env/bin/activate
-pip install ../_delphi_utils_python/.
-pip install .
+make install
 ```
 
+This command will install the package in editable mode, so you can make changes that
+will automatically propagate to the installed package. 
+
 All of the user-changable parameters are stored in `params.json`.
 
 The module has to request for each participating state's hospitalization data
@@ -32,35 +32,39 @@ the following:
 env/bin/python -m delphi_cdc_covidnet
 ```
 
-Once you are finished with the code, you can deactivate the virtual environment
-and (optionally) remove the environment itself.
+If you want to enter the virtual environment in your shell, 
+you can run `source env/bin/activate`. Run `deactivate` to leave the virtual environment. 
+
+Once you are finished, you can remove the virtual environment and 
+params file with the following:
 
 ```
-deactivate
-rm -r env
+make clean
 ```
 
 ## Testing the code
 
-To do a static test of the code style, it is recommended to run **pylint** on
-the module. To do this, run the following from the main module directory:
+To run static tests of the code style, run the following command:
 
 ```
-env/bin/pylint delphi_cdc_covidnet
+make lint
 ```
 
-The most aggressive checks are turned off; only relatively important issues
-should be raised and they should be manually checked (or better, fixed).
-
 Unit tests are also included in the module. To execute these, run the following
 command from this directory:
-(Note: the following command requires python 3.8, having any version less than 3.8 might
-fail some test cases. Please install it before running.)
+
 ```
-(cd tests && ../env/bin/pytest --cov=delphi_cdc_covidnet --cov-report=term-missing)
+make test
+```
+
+To run individual tests, run the following:
+
+```
+(cd tests && ../env/bin/pytest <your_test>.py --cov=delphi_cdc_covidnet --cov-report=term-missing)
 ```
 
 The output will show the number of unit tests that passed and failed, along
-with the percentage of code covered by the tests. None of the tests should
-fail and the code lines that are not covered by unit tests should be small and
-should not include critical sub-routines.
+with the percentage of code covered by the tests. 
+
+None of the linting or unit tests should fail, and the code lines that are not covered by unit tests should be small and
+should not include critical sub-routines. 

changehc/README.md

@@ -14,12 +14,12 @@ installed the common DELPHI tools, and then install the module and its
 dependencies. To do this, run the following code from this directory:
 
 ```
-python -m venv env
-source env/bin/activate
-pip install ../_delphi_utils_python/.
-pip install .
+make install
 ```
 
+This command will install the package in editable mode, so you can make changes that
+will automatically propagate to the installed package. 
+
 *Note*: you may need to install blas, in Ubuntu do
 ```
 sudo apt-get install libatlas-base-dev gfortran
@@ -33,37 +33,43 @@ the following:
 env/bin/python -m delphi_changehc
 ```
 
-Once you are finished with the code, you can deactivate the virtual environment
-and (optionally) remove the environment itself.
+If you want to enter the virtual environment in your shell, 
+you can run `source env/bin/activate`. Run `deactivate` to leave the virtual environment. 
+
+Once you are finished, you can remove the virtual environment and 
+params file with the following:
 
 ```
-deactivate
-rm -r env
+make clean
 ```
 
 ## Testing the code
 
-To do a static test of the code style, it is recommended to run **pylint** on
-the module. To do this, run the following from the main module directory:
+To run static tests of the code style, run the following command:
 
 ```
-env/bin/pylint delphi_changehc
+make lint
 ```
 
-The most aggressive checks are turned off; only relatively important issues
-should be raised and they should be manually checked (or better, fixed).
-
 Unit tests are also included in the module. To execute these, run the following
 command from this directory:
 
 ```
-(cd tests && ../env/bin/pytest --cov=delphi_changehc --cov-report=term-missing)
+make test
+```
+
+To run individual tests, run the following:
+
+```
+(cd tests && ../env/bin/pytest <your_test>.py --cov=delphi_changehc --cov-report=term-missing)
 ```
 
 The output will show the number of unit tests that passed and failed, along
-with the percentage of code covered by the tests. None of the tests should
-fail and the code lines that are not covered by unit tests should be small and
-should not include critical sub-routines.
+with the percentage of code covered by the tests. 
+
+None of the linting or unit tests should fail, and the code lines that are not covered by unit tests should be small and
+should not include critical sub-routines. 
+
 
 ## Code tour
 

claims_hosp/README.md

@@ -12,12 +12,12 @@ installed the common DELPHI tools, and then install the module and its
 dependencies. To do this, run the following code from this directory:
 
 ```
-python -m venv env
-source env/bin/activate
-pip install ../_delphi_utils_python/.
-pip install .
+make install
 ```
 
+This command will install the package in editable mode, so you can make changes that
+will automatically propagate to the installed package. 
+
 All of the user-changable parameters are stored in `params.json`. To execute
 the module and produce the output datasets (by default, in `receiving`), run
 the following:
@@ -26,37 +26,42 @@ the following:
 env/bin/python -m delphi_claims_hosp
 ```
 
-Once you are finished with the code, you can deactivate the virtual environment
-and (optionally) remove the environment itself.
+If you want to enter the virtual environment in your shell, 
+you can run `source env/bin/activate`. Run `deactivate` to leave the virtual environment. 
+
+Once you are finished, you can remove the virtual environment and 
+params file with the following:
 
 ```
-deactivate
-rm -r env
+make clean
 ```
 
 ## Testing the code
 
-To do a static test of the code style, it is recommended to run **pylint** on
-the module. To do this, run the following from the main module directory:
+To run static tests of the code style, run the following command:
 
 ```
-env/bin/pylint delphi_claims_hosp
+make lint
 ```
 
-The most aggressive checks are turned off; only relatively important issues
-should be raised and they should be manually checked (or better, fixed).
-
 Unit tests are also included in the module. To execute these, run the following
 command from this directory:
 
 ```
-(cd tests && ../env/bin/pytest --cov=delphi_claims_hosp --cov-report=term-missing)
+make test
+```
+
+To run individual tests, run the following:
+
+```
+(cd tests && ../env/bin/pytest <your_test>.py --cov=delphi_claims_hosp --cov-report=term-missing)
 ```
 
 The output will show the number of unit tests that passed and failed, along
-with the percentage of code covered by the tests. None of the tests should
-fail and the code lines that are not covered by unit tests should be small and
-should not include critical sub-routines.
+with the percentage of code covered by the tests. 
+
+None of the linting or unit tests should fail, and the code lines that are not covered by unit tests should be small and
+should not include critical sub-routines. 
 
 
 ## Code tour

combo_cases_and_deaths/README.md

@@ -10,12 +10,12 @@ installed the common DELPHI tools, and then install the module and its
 dependencies. To do this, run the following code from this directory:
 
 ```
-python -m venv env
-source env/bin/activate
-pip install ../_delphi_utils_python/.
-pip install .
+make install
 ```
 
+This command will install the package in editable mode, so you can make changes that
+will automatically propagate to the installed package. 
+
 All of the user-changable parameters are stored in `params.json`. To execute
 the module and produce the output datasets (by default, in `receiving`), run
 the following:
@@ -24,34 +24,39 @@ the following:
 env/bin/python -m delphi_combo_cases_and_deaths
 ```
 
-Once you are finished with the code, you can deactivate the virtual environment
-and (optionally) remove the environment itself.
+If you want to enter the virtual environment in your shell, 
+you can run `source env/bin/activate`. Run `deactivate` to leave the virtual environment. 
+
+Once you are finished, you can remove the virtual environment and 
+params file with the following:
 
 ```
-deactivate
-rm -r env
+make clean
 ```
 
 ## Testing the code
 
-To do a static test of the code style, it is recommended to run **pylint** on
-the module. To do this, run the following from the main module directory:
+To run static tests of the code style, run the following command:
 
 ```
-env/bin/pylint delphi_combo_cases_and_deaths
+make lint
 ```
 
-The most aggressive checks are turned off; only relatively important issues
-should be raised and they should be manually checked (or better, fixed).
-
 Unit tests are also included in the module. To execute these, run the following
 command from this directory:
 
 ```
-(cd tests && ../env/bin/pytest --cov=delphi_combo_cases_and_deaths --cov-report=term-missing)
+make test
+```
+
+To run individual tests, run the following:
+
+```
+(cd tests && ../env/bin/pytest <your_test>.py --cov=delphi_combo_cases_and_deaths --cov-report=term-missing)
 ```
 
 The output will show the number of unit tests that passed and failed, along
-with the percentage of code covered by the tests. None of the tests should
-fail and the code lines that are not covered by unit tests should be small and
-should not include critical sub-routines.
+with the percentage of code covered by the tests. 
+
+None of the linting or unit tests should fail, and the code lines that are not covered by unit tests should be small and
+should not include critical sub-routines.