reorganizing directories and updating Readme

NorthAtlanticBloom.yml

@@ -1,11 +1,17 @@
 name: NorthAtlanticBloom
 channels:
   - conda-forge
+  - defaults
 dependencies:
   - _libgcc_mutex=0.1=conda_forge
   - _openmp_mutex=4.5=2_gnu
+  - aiohttp=3.8.1=py39hb9d737c_1
+  - aiosignal=1.2.0=pyhd8ed1ab_0
   - alsa-lib=1.2.3.2=h166bdaf_0
+  - argopy=0.1.12=pyhd8ed1ab_0
   - asttokens=2.0.5=pyhd8ed1ab_0
+  - async-timeout=4.0.2=pyhd8ed1ab_0
+  - attrs=21.4.0=pyhd8ed1ab_0
   - backcall=0.2.0=pyh9f0ad1d_0
   - backports=1.0=py_2
   - backports.functools_lru_cache=1.6.4=pyhd8ed1ab_0
@@ -17,20 +23,21 @@ dependencies:
   - brotlipy=0.7.0=py39hb9d737c_1004
   - bzip2=1.0.8=h7f98852_4
   - c-ares=1.18.1=h7f98852_0
-  - ca-certificates=2022.5.18.1=ha878542_0
+  - ca-certificates=2022.6.15=ha878542_0
   - cached-property=1.5.2=hd8ed1ab_1
   - cached_property=1.5.2=pyha770c72_1
-  - certifi=2022.5.18.1=py39hf3d152e_0
+  - certifi=2022.6.15=py39hf3d152e_0
   - cffi=1.15.0=py39h4bc2ebd_0
   - cftime=1.6.0=py39hd257fcd_1
   - charset-normalizer=2.0.12=pyhd8ed1ab_0
   - click=8.1.3=py39hf3d152e_0
   - cloudpickle=2.1.0=pyhd8ed1ab_0
+  - cmcrameri=1.4=pyhd8ed1ab_0
   - cmocean=2.0=py_3
   - colorama=0.4.4=pyh9f0ad1d_0
   - colorspacious=1.1.2=pyh24bf2e0_0
-  - cryptography=37.0.2=py39hd97740a_0
-  - curl=7.83.1=h7bff187_0
+  - cryptography=36.0.0=py39h9ce1e76_0
+  - curl=7.83.1=h2283fc2_0
   - cycler=0.11.0=pyhd8ed1ab_0
   - cytoolz=0.11.2=py39hb9d737c_2
   - dask=2022.5.2=pyhd8ed1ab_0
@@ -41,6 +48,7 @@ dependencies:
   - distributed=2022.5.2=pyhd8ed1ab_0
   - docopt=0.6.2=py_1
   - entrypoints=0.4=pyhd8ed1ab_0
+  - erddapy=1.2.1=pyhd8ed1ab_0
   - executing=0.8.3=pyhd8ed1ab_0
   - expat=2.4.8=h27087fc_0
   - font-ttf-dejavu-sans-mono=2.37=hab24e00_0
@@ -52,15 +60,17 @@ dependencies:
   - fonts-conda-forge=1=0
   - fonttools=4.33.3=py39hb9d737c_0
   - freetype=2.10.4=h0708190_1
+  - frozenlist=1.3.0=py39hb9d737c_1
   - fsspec=2022.5.0=pyhd8ed1ab_0
   - gettext=0.19.8.1=h73d1719_1008
   - giflib=5.2.1=h36c2ea0_2
   - gst-plugins-base=1.20.2=hcf0ee16_0
   - gstreamer=1.20.2=hd4edc92_1
+  - gsw=3.4.0=py39hd257fcd_3
   - h5netcdf=1.0.0=pyhd8ed1ab_0
   - h5py=3.6.0=nompi_py39h7e08c79_100
   - hdf4=4.2.15=h10796ff_3
-  - hdf5=1.12.1=nompi_h2386368_104
+  - hdf5=1.12.1=nompi_h4df4325_104
   - heapdict=1.0.1=py_0
   - icu=69.1=h9c3ff4c_0
   - idna=3.3=pyhd8ed1ab_0
@@ -70,12 +80,13 @@ dependencies:
   - ipython=8.4.0=py39hf3d152e_0
   - jedi=0.18.1=py39hf3d152e_1
   - jinja2=3.1.2=pyhd8ed1ab_0
+  - joblib=1.1.0=pyhd8ed1ab_0
   - jpeg=9e=h166bdaf_1
   - jupyter_client=7.3.1=pyhd8ed1ab_0
   - jupyter_core=4.10.0=py39hf3d152e_0
   - keyutils=1.6.1=h166bdaf_0
   - kiwisolver=1.4.2=py39hf939315_1
-  - krb5=1.19.3=h3790be6_0
+  - krb5=1.19.3=h08a2579_0
   - lcms2=2.12=hddcbb42_0
   - ld_impl_linux-64=2.36.1=hea4e1c9_2
   - lerc=3.0=h9c3ff4c_0
@@ -85,11 +96,11 @@ dependencies:
   - libbrotlienc=1.0.9=h166bdaf_7
   - libcblas=3.9.0=14_linux64_openblas
   - libclang=13.0.1=default_hc23dcda_0
-  - libcurl=7.83.1=h7bff187_0
+  - libcurl=7.83.1=h2283fc2_0
   - libdeflate=1.10=h7f98852_0
   - libedit=3.1.20191231=he28a2e2_2
   - libev=4.33=h516909a_1
-  - libevent=2.1.10=h9b69904_4
+  - libevent=2.1.10=h28343ad_4
   - libffi=3.4.2=h7f98852_5
   - libgcc-ng=12.1.0=h8d9b700_16
   - libgfortran-ng=12.1.0=h69a702a_16
@@ -100,15 +111,15 @@ dependencies:
   - liblapack=3.9.0=14_linux64_openblas
   - libllvm13=13.0.1=hf817b99_2
   - libnetcdf=4.8.1=nompi_h329d8a1_102
-  - libnghttp2=1.47.0=h727a467_0
+  - libnghttp2=1.47.0=he49606f_0
   - libnsl=2.0.0=h7f98852_0
   - libogg=1.3.4=h7f98852_1
   - libopenblas=0.3.20=pthreads_h78a6416_0
   - libopus=1.3.1=h7f98852_1
   - libpng=1.6.37=h21135ba_2
-  - libpq=14.3=hd77ab85_0
+  - libpq=14.3=he2d8382_0
   - libsodium=1.0.18=h36c2ea0_1
-  - libssh2=1.10.0=ha56f1ee_2
+  - libssh2=1.10.0=ha35d2d1_2
   - libstdcxx-ng=12.1.0=ha89aaad_16
   - libtiff=4.4.0=h0fcbabc_0
   - libuuid=2.32.1=h7f98852_1000
@@ -118,7 +129,7 @@ dependencies:
   - libxcb=1.13=h7f98852_1004
   - libxkbcommon=1.0.3=he3ba5ed_0
   - libxml2=2.9.12=h885dcf4_1
-  - libzip=1.8.0=h4de3113_1
+  - libzip=1.8.0=h1c5bbd1_1
   - libzlib=1.2.12=h166bdaf_0
   - locket=1.0.0=pyhd8ed1ab_0
   - lz4=4.0.0=py39h029007f_2
@@ -128,17 +139,18 @@ dependencies:
   - matplotlib-base=3.5.2=py39h700656a_0
   - matplotlib-inline=0.1.3=pyhd8ed1ab_0
   - msgpack-python=1.0.4=py39hf939315_0
+  - multidict=6.0.2=py39hb9d737c_1
   - munkres=1.1.4=pyh9f0ad1d_0
-  - mysql-common=8.0.29=haf5c9bc_1
-  - mysql-libs=8.0.29=h28c427c_1
+  - mysql-common=8.0.29=h26416b9_1
+  - mysql-libs=8.0.29=hbc51c84_1
   - ncurses=6.3=h27087fc_1
   - nest-asyncio=1.5.5=pyhd8ed1ab_0
   - netcdf4=1.5.8=nompi_py39h64b754b_101
   - nspr=4.32=h9c3ff4c_1
   - nss=3.78=h2350873_0
   - numpy=1.22.4=py39hc58783e_0
   - openjpeg=2.4.0=hb52868f_1
-  - openssl=1.1.1o=h166bdaf_0
+  - openssl=3.0.5=h166bdaf_0
   - packaging=21.3=pyhd8ed1ab_0
   - pandas=1.4.2=py39h1832856_2
   - parso=0.8.3=pyhd8ed1ab_0
@@ -164,7 +176,7 @@ dependencies:
   - pyqtchart=5.12=py39h0fcd23e_8
   - pyqtwebengine=5.12.1=py39h0fcd23e_8
   - pysocks=1.7.1=py39hf3d152e_5
-  - python=3.9.13=h9a8a25e_0_cpython
+  - python=3.9.13=h2660328_0_cpython
   - python-dateutil=2.8.2=pyhd8ed1ab_0
   - python_abi=3.9=2_cp39
   - pytz=2022.1=pyhd8ed1ab_0
@@ -173,6 +185,7 @@ dependencies:
   - qt=5.12.9=h1304e3e_6
   - readline=8.1=h46c0cb4_0
   - requests=2.27.1=pyhd8ed1ab_0
+  - scikit-learn=1.1.1=py39h4037b75_0
   - scipy=1.8.1=py39he49c0e8_0
   - seawater=3.3.4=py_1
   - setuptools=62.3.2=py39hf3d152e_0
@@ -182,11 +195,13 @@ dependencies:
   - sqlite=3.38.5=h4ff8645_0
   - stack_data=0.2.0=pyhd8ed1ab_0
   - tblib=1.7.0=pyhd8ed1ab_0
+  - threadpoolctl=3.1.0=pyh8a188c0_0
   - tk=8.6.12=h27826a3_0
   - toolz=0.11.2=pyhd8ed1ab_0
   - tornado=6.1=py39hb9d737c_3
   - tqdm=4.64.0=pyhd8ed1ab_0
   - traitlets=5.2.2.post1=pyhd8ed1ab_0
+  - typing-extensions=4.2.0=hd8ed1ab_1
   - typing_extensions=4.2.0=pyha770c72_1
   - tzdata=2022a=h191b570_0
   - unicodedata2=14.0.0=py39hb9d737c_1
@@ -200,9 +215,10 @@ dependencies:
   - xorg-libxdmcp=1.1.3=h7f98852_0
   - xz=5.2.5=h516909a_1
   - yaml=0.2.5=h7f98852_2
+  - yarl=1.7.2=py39hb9d737c_2
   - zeromq=4.3.4=h9c3ff4c_1
   - zict=2.2.0=pyhd8ed1ab_0
   - zipp=3.8.0=pyhd8ed1ab_0
   - zlib=1.2.12=h166bdaf_0
   - zstd=1.5.2=h8a70e8d_1
-prefix: /autofs/nas1/home/isimoesdesousa/programs/mambaforge/envs/NorthAtlanticBloom
+prefix: /work/isimoesdesousa_umassd_edu/.conda/envs/NorthAtlanticBloom

README.md

@@ -23,31 +23,35 @@ Project Organization
     │
     ├── docs               <- A default Sphinx project; see sphinx-doc.org for details
     │
-    ├── notebooks          <- Jupyter notebooks. Naming convention is a number (for ordering),
-    │                         the creator's initials, and a short `-` delimited description, e.g.
-    │                         `1.0-jqp-initial-data-exploration`.
-    │
-    ├── references         <- Data dictionaries, manuals, and all other explanatory materials.
-    │
     ├── reports            <- Generated analysis as HTML, PDF, LaTeX, etc.
     │   └── figures        <- Generated graphics and figures to be used in reporting
     │
     └── src                <- Source code for use in this project.
         │
+        ├── 00-preprocess
+        │   │                 
+        │   └── 01-preprocess_external.py           <- preprocess external data
+        │
         ├── 01-model
         │   │                 
         │   ├── 01-initial_conditions.py            <- initial conditions for the fine-scale submesoscale simulation
         │   ├── 02-submesoscale.jl                  <- fine-scale submesoscale simulation
         │   ├── 03-initial_conditions_coarse.py     <- initial conditions for the coarse-resolution simulations
-        │   ├── 04-coarse_no_mle.jl                 <- coarse-resolution simulation with no MLE parameterization
-        │   ├── 05-coarse_mle.jl                    <- coarse-resolution simulation with MLE parameterization
-        │   └── cumulative_vertical_integration.jl  <- function used for initial geostrophic velocities
+        │   ├── 04-coarse_averaging.jl              <- coarse-resolution simulation that prescribes restratification (NVF)
+        │   ├── 05-coarse_mle.jl                    <- coarse-resolution simulation with MLE parameterization (MLE)
+        │   ├── cumulative_vertical_integration.jl  <- function used for initial geostrophic velocities
+        │   ├── mle_parameterization.jl             <- function for computing the eddy stream function from Fox-Kemper et al. (2011)
+        │   ├── Manifest.toml                       <- manifest file with for the Julia packages
+        │   └── Project.toml                        <- project file with for the Julia packages
         │   
-        ├── 02-analysis
-        │   └── 01-analysis.py                      <- analyze the model output and generate processed data        
-        │
-        └── 03-visualization  <- Scripts to create exploratory and results oriented visualizations
-            └── 01-visualize.py
+        └── 02-analysis
+            ├── 01-video.py                         <- code for generating frames for the video
+            ├── 02-3D_plots.py                      <- 3D box plots for w and Ro
+            ├── 03-Ro_restratification.py           <- comparison for the evolution of Ro and restratification
+            ├── 04-biogeochemistry.py               <- comparing new production between simulations
+            ├── 05-nitrate_flux.py                  <- comparing nitrate flux between simulations
+            └── cmaps.py                            <- extra colormaps     
+
 
 
 --------