Merge pull request #88 from JoyMonteiro/develop

Refactor of init code

.appveyor.yml

@@ -4,8 +4,8 @@ environment:
   matrix:
     - PYTHON_VERSION: "3.6"
       MINICONDA: "C:\\Miniconda36-x64"
-#    - PYTHON_VERSION: "3.5"
-#      MINICONDA: "C:\\Miniconda35-x64"
+    - PYTHON_VERSION: "3.7"
+      MINICONDA: "C:\\Miniconda37-x64"
 
 platform:
   - x64
@@ -42,15 +42,15 @@ install:
   - conda install libpython
   - python -m pip install -r requirements_dev.txt
   - conda upgrade pip setuptools wheel
-#  - set COMPILER_PATH=C:\\msys64\\mingw64\\bin\\
+# - set COMPILER_PATH=C:\\msys64\\mingw64\\bin\\
 
 build_script:
   - bash -c "cd /c/projects/climt/; python setup.py develop"
 #  - bash -c "cd /c/projects/climt/; python setup.py build --compiler=mingw32"
 
 test_script:
   - conda install pytest
-  - bash -c "cd /c/projects/climt; py.test"
+  - bash -c "cd /c/projects/climt; py.test -v"
 # - bash -c "cd /c/projects/climt; find . |grep _components"
 
 after_test:

.travis.yml

@@ -5,13 +5,11 @@ services: docker
 language: python
 python: 3.6
 
-  #branches:
-  #    except:
-  #    - sympl-0.4.0
 
 cache:
     - pip
     - directories: ~/build/CliMT/climt/climt/_lib/Linux
+    - directories: ~/build/CliMT/climt/climt/_lib/Darwin
 env:
     global:
       - TWINE_USERNAME=joy.merwin
@@ -30,14 +28,29 @@ allow_failures:
 
 before_install:
 - if [[ "$TRAVIS_OS_NAME" == "linux" ]]; then sudo apt-get install gfortran; fi
-- if [[ "$TRAVIS_OS_NAME" == "osx" ]]; then curl -sSL https://rvm.io/mpapis.asc | gpg --import -; fi
-- if [[ "$TRAVIS_OS_NAME" == "osx" ]]; then rvm get stable                 ; fi
-- if [[ "$TRAVIS_OS_NAME" == "osx" ]]; then brew update                    ; fi
-- if [[ "$TRAVIS_OS_NAME" == "osx" ]]; then brew cask uninstall oclint     ; fi
-- if [[ "$TRAVIS_OS_NAME" == "osx" ]]; then brew install gcc               ; fi
-- if [[ "$TRAVIS_OS_NAME" == "osx" ]]; then brew upgrade python            ; fi
-- if [[ "$TRAVIS_OS_NAME" == "osx" ]]; then python3 -m venv climt_venv     ; fi
-- if [[ "$TRAVIS_OS_NAME" == "osx" ]]; then source climt_venv/bin/activate ; fi
+- |
+    if [[ "$TRAVIS_OS_NAME" == "osx" ]]; 
+    then curl -sSL https://rvm.io/mpapis.asc | gpg --import -
+    rvm get stable
+    brew update
+    sudo softwareupdate -i "Command Line Tools (macOS High Sierra version 10.13) for Xcode-9.4"
+    brew cask uninstall oclint
+    brew install gcc@6
+    brew install md5sha1sum
+    fi
+- if [[ "$TRAVIS_PYTHON_VERSION" == "2.7" ]]; then
+      wget https://repo.continuum.io/miniconda/Miniconda2-latest-MacOSX-x86_64.sh -O miniconda.sh;
+    else
+      wget https://repo.continuum.io/miniconda/Miniconda3-latest-MacOSX-x86_64.sh -O miniconda.sh;
+    fi
+- |
+    if [[ "$TRAVIS_OS_NAME" == "osx" ]]; then  
+    bash miniconda.sh -b -p $HOME/miniconda
+    export PATH="$HOME/miniconda/bin:$PATH"
+    hash -r
+    conda config --set always_yes yes --set changeps1 no
+    conda info -a
+    fi
 
 install:
 - python -m pip install -r requirements_dev.txt
@@ -76,6 +89,34 @@ jobs:
       env: TOXENV=py27 CLIMT_ARCH=Linux
       script:
           - tox -e ${TOXENV}
+    - stage: big tests
+      dist: xenial
+      python: "3.7"
+      env: TOXENV=py37 CLIMT_ARCH=Linux
+      script:
+          - tox -e ${TOXENV}
+    - stage: big tests
+      os: osx
+      language: generic
+      env: PYTHON_VERSION=3.6 TOXENV=py36 CLIMT_ARCH=Darwin OMP_NUM_THREADS=1
+      install:
+          - conda create -q -n test-environment python=$PYTHON_VERSION
+          - source activate test-environment
+          - python -m pip install -r requirements_dev.txt
+          - python -m pip install -U tox
+      script:
+          - travis_wait 50 tox -e ${TOXENV}
+    - stage: big tests
+      os: osx
+      language: generic
+      env: PYTHON_VERSION=3.7 TOXENV=py37 CLIMT_ARCH=Darwin OMP_NUM_THREADS=1
+      install:
+          - conda create -q -n test-environment python=$PYTHON_VERSION
+          - source activate test-environment
+          - python -m pip install -r requirements_dev.txt
+          - python -m pip install -U tox
+      script:
+          - travis_wait 50 tox -e ${TOXENV}
     - stage: wheels
       env: CLIMT_ARCH=Linux CIBW_SKIP='cp33-* cp36-* cp35-* cp34-* cp37-* cp27-manylinux1_i686' CIBW_BEFORE_BUILD="{pip} install pandas==0.20.3"
       script:
@@ -106,18 +147,40 @@ jobs:
             python -m pip install twine
             python -m twine upload wheelhouse/*.whl
             fi
-    #- stage: wheels
-    #  os: osx
-    #  language: generic
-    #  env: CLIMT_ARCH=Darwin CIBW_SKIP='cp33-* cp35-* cp34-* cp27-* cp36-manylinux1_i686'
-    #  script:
-    #    - |
-    #        if [[ $TRAVIS_TAG ]]; then
-    #        python -m pip install cibuildwheel
-    #        travis_wait 50 cibuildwheel --output-dir wheelhouse
-    #        python -m pip install twine
-    #        python -m twine upload wheelhouse/*.whl
-    #        fi
+    - stage: wheels
+      env: CLIMT_ARCH=Linux CIBW_SKIP='cp33-* cp35-* cp34-* cp27-* cp36-*  cp37-manylinux1_i686'
+      script:
+        - |
+            if [[ $TRAVIS_TAG ]]; then
+            python -m pip install cibuildwheel
+            cibuildwheel --output-dir wheelhouse
+            python -m pip install twine
+            python -m twine upload wheelhouse/*.whl
+            fi
+    - stage: wheels
+      os: osx
+      language: generic
+      env: CLIMT_ARCH=Darwin CIBW_SKIP='cp33-* cp35-* cp34-* cp27-* cp37-*'
+      script:
+        - |
+            if [[ $TRAVIS_TAG ]]; then
+            python -m pip install cibuildwheel
+            travis_wait 50 cibuildwheel --output-dir wheelhouse
+            python -m pip install twine
+            python -m twine upload wheelhouse/*.whl
+            fi
+    - stage: wheels
+      os: osx
+      language: generic
+      env: CLIMT_ARCH=Darwin CIBW_SKIP='cp33-* cp35-* cp34-* cp27-* cp36-*'
+      script:
+        - |
+            if [[ $TRAVIS_TAG ]]; then
+            python -m pip install cibuildwheel
+            travis_wait 50 cibuildwheel --output-dir wheelhouse
+            python -m pip install twine
+            python -m twine upload wheelhouse/*.whl
+            fi
 
 
 deploy:

HISTORY.rst

@@ -5,7 +5,8 @@ History
 Latest
 ------
 
-
+* CI Testing for Mac and py37 added.
+* Refactored initialisation code
 * Enable the McICA version of RRTMG Longwave for consistency
   with the Shortwave component.
 * Fix bugs in IceSheet
@@ -24,6 +25,9 @@ Breaking Changes
 
 * The flux outputs of GrayLongwaveRadiation have been renamed to eliminate
   `on_interface_levels` to keep consistency with other components.
+* All arrays are now 3/2d by default based on their expected dimensions.
+* horizontal dimensions are now `model_longitude`, `model_latitude`, but inputs
+  used by components remain the same (`latitude`, `longitude`).
 
 
 

climt/_components/dcmip/component.py

@@ -5,9 +5,10 @@
 import numpy as np
 try:
     from . import _dcmip
-except ImportError:
+except ImportError as error:
     logging.warning(
         'Import Failed. DCMIP initial conditions will not be available.')
+    print(error)
 
 
 class DcmipInitialConditions(DiagnosticComponent):

climt/_components/dry_convection/component.py

@@ -12,20 +12,20 @@ class DryConvectiveAdjustment(Stepper):
     input_properties = {
         'air_temperature': {
             'units': 'degK',
-            'dims': ['*', 'mid_levels'],
+            'dims': ['mid_levels', '*'],
         },
         'air_pressure': {
             'units': 'Pa',
-            'dims': ['*', 'mid_levels'],
+            'dims': ['mid_levels', '*'],
         },
         'air_pressure_on_interface_levels': {
             'units': 'Pa',
-            'dims': ['*', 'interface_levels'],
+            'dims': ['interface_levels', '*'],
             'alias': 'P_int',
         },
         'specific_humidity': {
             'units': 'kg/kg',
-            'dims': ['*', 'mid_levels'],
+            'dims': ['mid_levels', '*'],
         },
     }
 
@@ -54,30 +54,28 @@ def array_call(self, state, time_step):
             self.output_properties, state, self.input_properties
         )
 
-        output_temp = output_arrays['air_temperature']
-        output_temp[:] = state['air_temperature']
+        output_temperature = output_arrays['air_temperature']
+        output_temperature[:] = state['air_temperature']
 
         output_q = output_arrays['specific_humidity']
         output_q[:] = q
 
         rd_cp = self.gas_constant(q)/self.heat_capacity(q)
         theta = state['air_temperature']*(self._Pref/state['air_pressure'])**rd_cp
-        theta_q = theta*(1 + output_q*self._Rv/self._Rdair - output_q)
 
-        # print('initial theta:', theta)
+        num_levels = q.shape[0]
 
-        num_levels = q.shape[-1]
-
-        for column in range(q.shape[0]):
+        for column in range(q.shape[-1]):
             for level in range(num_levels-1, -1, -1):
 
-                dp = state['P_int'][column, :-1] - state['P_int'][column, 1:]
-                theta_sum = np.cumsum(theta_q[column, level::])
+                dp = state['P_int'][:-1, column] - state['P_int'][1:, column]
+                theta_q = theta*(1 + output_q*self._Rv/self._Rdair - output_q)
+                theta_sum = np.cumsum(theta_q[level::, column])
                 divisor = np.arange(1, num_levels - level+1)
 
                 theta_avg = (theta_sum/divisor)[1::]
 
-                theta_lesser = (theta_avg > theta_q[column, level+1::])
+                theta_lesser = (theta_avg > theta_q[level+1::, column])
                 if np.sum(theta_lesser) == 0:
                     continue
 
@@ -90,36 +88,28 @@ def array_call(self, state, time_step):
                     continue
                 stable_level = level + convect_to_level
 
-                q_conv = output_q[column, level:stable_level]
-                t_conv = output_temp[column, level:stable_level]
+                q_conv = output_q[level:stable_level, column]
+                t_conv = output_temperature[level:stable_level, column]
                 dp_conv = dp[level:stable_level]
-                p_conv_high = state['P_int'][column, level]
-                p_conv_low = state['P_int'][column, stable_level]
+                p_conv_high = state['P_int'][level, column]
+                p_conv_low = state['P_int'][stable_level, column]
 
                 enthalpy = self.heat_capacity(q_conv)*t_conv
                 integral_enthalpy = np.sum(enthalpy*dp_conv)
                 mean_conv_q = np.sum(q_conv*dp_conv)/(p_conv_high - p_conv_low)
 
-                output_q[column, level:stable_level] = mean_conv_q
+                output_q[level:stable_level, column] = mean_conv_q
 
                 rdcp_conv = self.gas_constant(mean_conv_q)/self.heat_capacity(mean_conv_q)
 
                 theta_coeff = (
-                    state['air_pressure'][column, level:stable_level]/self._Pref)**rdcp_conv
+                    state['air_pressure'][level:stable_level, column]/self._Pref)**rdcp_conv
 
                 integral_theta_den = np.sum(self.heat_capacity(q_conv)*theta_coeff*dp_conv)
 
                 mean_theta = integral_enthalpy/integral_theta_den
 
-                output_temp[column, level:stable_level] = mean_theta*theta_coeff
-
-        # dp = (state['P_int'][0, :-1] - state['P_int'][0, 1:])/(state['P_int'][0, 0] - state['P_int'][0, -1])
-        # print('Initial Enthalpy: ', np.sum(self.heat_capacity(state['specific_humidity'])*state['air_temperature']*dp))
-        # print('Final Enthalpy: ', np.sum(self.heat_capacity(output_q)*output_temp*dp))
-        # rd_cp = self.gas_constant(output_q)/self.heat_capacity(output_q)
-        # theta = output_temp*(self._Pref/state['air_pressure'])**rd_cp
-
-        # print('final theta: ', theta)
+                output_temperature[level:stable_level, column] = mean_theta*theta_coeff
 
         return {}, output_arrays
 

climt/_components/emanuel/component.py

@@ -6,11 +6,12 @@
 import logging
 try:
     from . import _emanuel_convection
-except ImportError:
+except ImportError as error:
     logging.warning(
         'Import failed. Emanuel Convection is likely not compiled and will not '
         'be available.'
     )
+    print(error)
 
 
 class EmanuelConvection(ImplicitTendencyComponent):