SIP78 Convert switches to run time options (#96)

* Initial commit

* Removes makedepend info

* Code cleanup

* Splits cli into .h and .c; also code cleanup

* Adds back namelistInputs.c temporarily

* Removes namelistInput.c after merrge with master

* Tweaks check order in readInputFile

* Makes Context struct extern in header

* Fixes return codes for help and version

* Adds config file to help CLion users

* added quickstart (#101)

* more helpful error reading / writing

* Update format for clang-format

* Moves version string to new version.h

* Fixes merge error

---------

Co-authored-by: David LeBauer <dlebauer@gmail.com>

Author: Alomir

CMakeLists.txt

@@ -0,0 +1,37 @@
+# This file is here to make CLion users' lives better, but it is not complete.
+# One cannot build sipnet from this file. But, it does let CLion do a much
+# better job with code analysis.
+
+# As C files are added and/or removed, this file should be updated.
+
+cmake_minimum_required(VERSION 3.30)
+project(sipnet C)
+
+set(CMAKE_C_STANDARD 23)
+
+include_directories(src)
+include_directories(src/common)
+include_directories(src/sipnet)
+include_directories(tests)
+include_directories(tests/sipnet/test_events_infrastructure)
+include_directories(tests/sipnet/test_events_types)
+include_directories(tests/sipnet/test_bugfixes)
+include_directories(tests/sipnet/test_sipnet_infrastructure)
+include_directories(tests/utils)
+
+add_compile_options(-Wall -Wpedantic -Werror)
+
+add_library(commonlib
+        src/common/spatialParams.c
+        src/common/util.c
+)
+
+add_library(sipnetlib
+        src/sipnet/cli.c
+        src/sipnet/context.c
+        src/sipnet/events.c
+        src/sipnet/frontend.c
+        src/sipnet/outputItems.c
+        src/sipnet/runmean.c
+        src/sipnet/sipnet.c
+)

Makefile

@@ -7,11 +7,11 @@ LIB_DIR=./libs
 LDFLAGS=-L$(LIB_DIR)
 
 # Main executables
-COMMON_CFILES:=util.c namelistInput.c modelParams.c
+COMMON_CFILES:=util.c modelParams.c
 COMMON_CFILES:=$(addprefix src/common/, $(COMMON_CFILES))
 COMMON_OFILES=$(COMMON_CFILES:.c=.o)
 
-SIPNET_CFILES:=sipnet.c frontend.c runmean.c outputItems.c events.c
+SIPNET_CFILES:=sipnet.c frontend.c runmean.c outputItems.c events.c context.c cli.c
 SIPNET_CFILES:=$(addprefix src/sipnet/, $(SIPNET_CFILES))
 SIPNET_OFILES=$(SIPNET_CFILES:.c=.o)
 SIPNET_LIBS=-lsipnet_common

docs/README.md

@@ -4,6 +4,26 @@ SIPNET (Simplified Photosynthesis and Evapotranspiration Model) is an ecosystem
 carbon and water dynamics. Originally developed for assimilation of eddy covariance flux data in forest ecosystems, 
 current development is focused on representing carbon balance and GHG fluxes and agricultural management practices.
 
+## Quick Start
+
+1. Clone the repository:
+   ```bash
+   git clone https://github.com/PecanProject/sipnet.git
+   cd sipnet
+   ```
+2. Build the SIPNET executable:
+   ```bash
+    make
+    ```
+3. Run a test simulation:
+   ```bash
+   ./src/sipnet -i tests/smoke/sipnet.in
+   ```
+4. Check the output:
+   ```bash
+   cat tests/smoke/niwot.out
+   ```
+
 ## Getting Started
 
 ### Installing

src/common/exitCodes.h

@@ -21,7 +21,8 @@ typedef enum {
   EXIT_CODE_UNKNOWN_EVENT_TYPE_OR_PARAM = 4,
   EXIT_CODE_INPUT_FILE_ERROR = 5,
   EXIT_CODE_FILE_OPEN_OR_READ_ERROR = 6,
-  EXIT_CODE_INTERNAL_ERROR = 7
+  EXIT_CODE_INTERNAL_ERROR = 7,
+  EXIT_CODE_BAD_CLI_ARGUMENT = 8
 } exit_code_t;
 
 #endif