Merge pull request #16 from junhyukjeon/master

Revert branch 'master' to 3PG model

.github/workflows/CI.yml

@@ -0,0 +1,38 @@
+name: CI
+on:
+  push:
+    branches:
+      - master
+    tags: '*'
+  pull_request:
+concurrency:
+  # Skip intermediate builds: always.
+  # Cancel intermediate builds: only if it is a pull request build.
+  group: ${{ github.workflow }}-${{ github.ref }}
+  cancel-in-progress: ${{ startsWith(github.ref, 'refs/pull/') }}
+jobs:
+  test:
+    name: Julia ${{ matrix.version }} - ${{ matrix.os }} - ${{ matrix.arch }} - ${{ github.event_name }}
+    runs-on: ${{ matrix.os }}
+    strategy:
+      fail-fast: false
+      matrix:
+        version:
+          - '1.6'
+          - '1.7'
+          - 'nightly'
+        os:
+          - ubuntu-latest
+        arch:
+          - x64
+    steps:
+      - uses: actions/checkout@v2
+      - uses: julia-actions/setup-julia@v1
+        with:
+          version: ${{ matrix.version }}
+          arch: ${{ matrix.arch }}
+      - uses: julia-actions/cache@v1
+      - uses: julia-actions/julia-buildpkg@v1
+        env:
+          PYTHON: ""
+      - uses: julia-actions/julia-runtest@v1

.github/workflows/CompatHelper.yml

@@ -0,0 +1,16 @@
+name: CompatHelper
+on:
+  schedule:
+    - cron: 0 0 * * *
+  workflow_dispatch:
+jobs:
+  CompatHelper:
+    runs-on: ubuntu-latest
+    steps:
+      - name: Pkg.add("CompatHelper")
+        run: julia -e 'using Pkg; Pkg.add("CompatHelper")'
+      - name: CompatHelper.main()
+        env:
+          GITHUB_TOKEN: ${{ secrets.GITHUB_TOKEN }}
+          COMPATHELPER_PRIV: ${{ secrets.DOCUMENTER_KEY }}
+        run: julia -e 'using CompatHelper; CompatHelper.main()'

.github/workflows/TagBot.yml

@@ -0,0 +1,15 @@
+name: TagBot
+on:
+  issue_comment:
+    types:
+      - created
+  workflow_dispatch:
+jobs:
+  TagBot:
+    if: github.event_name == 'workflow_dispatch' || github.actor == 'JuliaTagBot'
+    runs-on: ubuntu-latest
+    steps:
+      - uses: JuliaRegistries/TagBot@v1
+        with:
+          token: ${{ secrets.GITHUB_TOKEN }}
+          ssh: ${{ secrets.DOCUMENTER_KEY }}

README.md

@@ -1 +1,3 @@
-# Poplar
+# Poplar
+
+[![Build Status](https://github.com/junhyukjeon/Poplar.jl/actions/workflows/CI.yml/badge.svg?branch=master)](https://github.com/junhyukjeon/Poplar.jl/actions/workflows/CI.yml?query=branch%3Amaster)

src/Poplar.jl

@@ -14,7 +14,7 @@ include("silviculture/silviculture.jl")
 @system Model(Atmosphere, Calendar, Morphology, Phenology, Physiology, Rhizosphere, Silviculture, Controller)
 
 weather = Poplar.loadwea(Poplar.datapath("2007.wea"), tz"Asia/Seoul")
-CUH = Poplar.loadwea(Poplar.datapath("CUH.wea"), tz"UTC-8")
+CUH = Poplar.loadwea(Poplar.datapath("CUH.wea"), tz"America/Los_Angeles")
 
 export Model
 

src/atmosphere/atmosphere.jl

@@ -2,7 +2,4 @@ include("sun.jl")
 include("vaporpressure.jl")
 include("weather.jl")
 
-"""
-Parent system for Sun, VaporPressure, and Weather.
-"""
 @system Atmosphere(Sun, VaporPressure, Weather)

src/atmosphere/sun.jl

@@ -1,7 +1,3 @@
-"""
-Calculates variables related to solar position.
-Perhaps consider moving latitude, longitude, altitude to another system?
-"""
 @system Sun begin
     lat: latitude => 47.66u"°" ~ preserve(u"°", parameter)
     long: longitude => 122.29u"°" ~ preserve(u"°", parameter)
@@ -19,8 +15,8 @@ Perhaps consider moving latitude, longitude, altitude to another system?
     # Solar Coordinates #
     #####################
 
-    # HACK always use degrees for consistency and easy tracing
-    # FIXME pascal version of LightEnv uses iqbal()
+    #HACK always use degrees for consistency and easy tracing
+    #FIXME pascal version of LightEnv uses iqbal()
     declination_angle(declination_angle_spencer) ~ track(u"°")
 
     # Goudriaan 1977
@@ -35,20 +31,20 @@ Perhaps consider moving latitude, longitude, altitude to another system?
         23.5u"°" * cos(g)
     end ~ track(u"°")
 
-    # Iqbal (1983) Pg 10 Eqn 1.3.3, and sundesign.com.
+    # Iqbal (1983) Pg 10 Eqn 1.3.3, and sundesign.com
     declination_angle_iqbal(d) => begin
         g = 2pi * (d + 284u"d") / 365u"d"
         23.45u"°" * sin(g)
     end ~ track(u"°")
 
-    # Campbell and Norman, p168.
+    # Campbell and Norman, p168
     declination_angle_campbell(d) => begin
         a = deg2rad(356.6 + 0.9856u"d^-1" * d)
         b = deg2rad(278.97 + 0.9856u"d^-1" * d + 1.9165sin(a))
         asind(0.39785sin(b))
     end ~ track(u"°")
 
-    # Spencer equation, Iqbal (1983) Pg 7 Eqn 1.3.1. Most accurate among all.
+    # Spencer equation, Iqbal (1983) Pg 7 Eqn 1.3.1. Most accurate among all
     declination_angle_spencer(d) => begin
         # gamma: day angle
         g = 2pi * (d - 1u"d") / 365u"d"

src/atmosphere/vaporpressure.jl

@@ -1,6 +1,3 @@
-"""
-Calculates vapor pressure.
-"""
 @system VaporPressure begin
     # Campbell and Norman (1998), p 41 Saturation vapor pressure in kPa
     a => 0.611 ~ preserve(u"kPa", parameter)
@@ -14,18 +11,18 @@ Calculates vapor pressure.
 
     # slope of the sat vapor pressure curve: first order derivative of Es with respect to T
     Δ(es, b, c; T(u"°C")): saturation_slope_delta => (e = es(T); t = Cropbox.deunitfy(T); e*(b*c)/(c+t)^2 / u"K") ~ call(u"kPa/K")
-    sat_slope(Δ; T(u"°C"), P(u"kPa")): saturation_slope => Δ(T) / P ~ call(u"K^-1")
+    ss(Δ; T(u"°C"), P(u"kPa")): saturation_slope => Δ(T) / P ~ call(u"K^-1")
 
     #==============
     VPD Calculation
     ==============#
 
     "VPD"
-    VPD(T_air, RH, D): vapor_pressure_deficit => D(T_air, RH) ~ track(u"kPa")
+    VPD(T_air, RH, D) => D(T_air, RH) ~ track(u"kPa")
 
     "Vapor pressure saturation slope delta"
     VPD_Δ(T_air, Δ): vapor_pressure_saturation_slope_delta => Δ(T_air) ~ track(u"kPa/K")
 
     "Vapor pressure saturation slope"
-    VPD_s(T_air, P_air, sat_slope): vapor_pressure_saturation_slope => sat_slope(T_air, P_air) ~ track(u"K^-1")
+    VPD_s(T_air, P_air, ss): vapor_pressure_saturation_slope => ss(T_air, P_air) ~ track(u"K^-1")
 end

src/atmosphere/weather.jl

@@ -1,11 +1,10 @@
-"""
-Weather
-"""
 @system Weather begin
     #=========
     Parameters
     =========#
 
+    # DataFrame containing all hourly weather data should be
+    # assigned to this variable during configuration.
     "Data"
     data ~ provide(init=time, parameter)
 
@@ -20,7 +19,7 @@ Weather
     ================#
 
     "Solar Radiation"
-    solar_radiation ~ drive(from=data, by=:SolRad, u"W/m^2")
+    solrad: solar_radiation ~ drive(from=data, by=:SolRad, u"W/m^2")
 
     "Relative Humidity"
     RH: relative_humidity ~ drive(from=data, by=:RH, u"percent")

src/calendar/calendar.jl

@@ -1,20 +1,15 @@
 """
-Calendar keeps track of date and time-related variables.
+Calendar keeps track of date and time throughout simulation.
 """
 @system Calendar begin
-    "Initial date"
     init ~ preserve::datetime(extern, parameter)
 
-    "Last date"
     last => nothing ~ preserve::datetime(extern, parameter, optional)
 
-    "Time"
     time(t0=init, t=context.clock.time) => t0 + convert(Cropbox.Dates.Second, t) ~ track::datetime
 
-    "Date"
     date(time) => Cropbox.Dates.Date(time) ~ track::date
 
-    "Timestep"
     step(context.clock.step) ~ preserve(u"hr")
 
     stop(time, last) => begin
@@ -29,9 +24,7 @@ Calendar keeps track of date and time-related variables.
         end
     end ~ preserve::int(round, optional)
 
-    "Day of year"
     d(time) => Dates.dayofyear(time) ~ track::int(u"d")
 
-    "Hour of day"
     h(time) => Dates.hour(time) ~ track::int(u"hr")
 end

src/config/config.jl

@@ -9,15 +9,15 @@ include("../rhizosphere/soil.jl")
 # Weather data MUST include the date range specified.
 config_Calendar = @config(
     :Calendar => (
-        init = ZonedDateTime(2014, 4, 5, tz"UTC-8"),
-        last = ZonedDateTime(2021, 12, 31, tz"UTC-8"),
+        init = ZonedDateTime(2014, 4, 5, tz"America/Los_Angeles"),
+        last = ZonedDateTime(2021, 12, 31, tz"America/Los_Angeles"),
     )
 )
 
 # Weather data must be included.
 config_Atmosphere = @config(
     :Atmosphere => (
-        data = Poplar.loadwea(Poplar.datapath("CUH.wea"), tz"UTC-8"),
+        data = Poplar.loadwea(Poplar.datapath("CUH.wea"), tz"America/Los_Angeles"),
     )
 )