Merge pull request #222 from ACCESS-Community-Hub/prerelease

Prerelease

Author: rbeucher

ACDD_conf.yaml

@@ -97,7 +97,7 @@ cmor:
     grids: "ACDD_grids.json"
 # Additional NCI information:
     # NCI project to charge compute; $PROJECT = your default project
-    project: v45 
+    project: <proj-id> 
     # additional NCI projects to be included in the storage flags, comma separated list
     addprojs: []
     # queue and memory (GB) per CPU (depends on queue),

CMIP6_conf.yaml

@@ -90,7 +90,7 @@ cmor:
     grids: CMIP6_grids.json
   # Additional NCI information:
     # NCI project to charge compute; $PROJECT = your default project
-    project: v45
+    project: <proj-id> 
     # additional NCI projects to be included in the storage flags, comma separated list
     addprojs: []
     # queue and memory (GB) per CPU (depends on queue) 

conda/environment.yaml

@@ -6,3 +6,18 @@ dependencies:
   - anaconda-client
   - conda-build
   - conda-verify
+  - python #=3.11
+  - click
+  - xarray>=2024.05.0
+  - cmor  #=3.11.0
+  - numpy
+  - dask
+  - pyyaml
+  - cftime
+  - python-dateutil
+  - metpy
+  - gsw
+  - pytest
+  - pyfakefs
+  - coverage
+  - codecov

conda/meta.yaml

@@ -1,14 +1,14 @@
 package:
     name: mopper 
     #version: "{{ environ.get('GIT_DESCRIBE_TAG', '1.0') }}"
-    version: '1.2.0'
+    version: '1.3.0'
 #source:
 # path: ../.
 
 source:
   #url: https://github.com/ACCESS-Hive/ACCESS-MOPPeR/archive/refs/tags/{{ environ.get('RELEASE_VERSION') }}.tar.gz
   git_url: https://github.com/ACCESS-Hive/ACCESS-MOPPeR.git
-  git_tag: "1.2.0"
+  git_tag: "1.3.0"
   #git_rev: "1.1.0"
   #git_depth: 1 # (Defaults to -1/not shallow)
 
@@ -28,7 +28,7 @@ requirements:
         - python
         - click
         - xarray>=2024.05.0
-        - cmor
+        - cmor   #=3.11.0
         - numpy
         - dask
         - pyyaml

docs/cmor_conf.yaml

@@ -101,7 +101,7 @@ cmor:
     # walltime in "hh:mm:ss"
     walltime: '8:00:00'
     mode: custom
-    # conda_env to use by default hh5 analysis3-unstable
+    # conda_env to use by default xp65 analysis3 (stable)
     # as this has the code and all dependecies installed
     # you can override that by supplying the env to pass to "source"
     # Ex

docs/mopdb_command.rst

@@ -209,7 +209,7 @@ The `del` sub-command allows to delete one or more records from the selected tab
 Selecting a database
 --------------------
 
-By default, if using the package installed in the hh5 conda environment, mopdb will use the `access.db` database which comes with the package.
+By default mopdb will use the `access.db` database which comes with the installed package.
 If a user wants to modify the database, they will need to get a copy of the official database or define a new one from scratch as shown above.
 Then the `--dbname <database-name>` option can be used to select the custom database.
 

docs/output.rst

@@ -61,18 +61,18 @@ This folder will contain the following files:
     | #!/bin/bash
     | #PBS -P v45
     | #PBS -q hugemem
-    | #PBS -l storage=gdata/hh5+gdata/ua8+scratch/ly62+scratch/v45+gdata/v45
+    | #PBS -l storage=gdata/xp65+gdata/ua8+scratch/ly62+scratch/v45+gdata/v45
     | #PBS -l ncpus=24,walltime=12:00:00,mem=768GB,wd
     | #PBS -j oe
     | #PBS -o /scratch/v45/pxp581/MOPPER_output/ashwed1980/job_output.OU
     | #PBS -N mopper_ashwed1980
     |
-    | # the code assumes you are running this on gadi and have access to the hh5 project modules
+    | # the code assumes you are running this on gadi and have access to the xp65 project modules
     | # if this is not the case make sure you have loaded alternative python modules
     | # see https://github.com/ACCESS-Community-Hub/ACCESS-MOPPeR/blob/main/requirements.txt
     | # for a list of packages
     |
-    | module use /g/data/hh5/public/modules
+    | module use /g/data/xp65/public/modules
     | module load conda/analysis3
     | source mopper_env/bin/activate # if using conda option
     |

docs/overview.rst

@@ -2,7 +2,10 @@ Install
 =======
 
 ACCESS-MOPPeR is available at NCI on the hh5 conda environments.
-To access a more recent version, you can create a custom conda environment and install mopper following these steps:
+As these will be soon phased out you will have to create your own custom conda environment or local installation.
+We reccommed to use the ACCESS-NRI conda envs (xp65) as base, as these will have most of the requirements available. 
+
+To create a custom conda environment and install mopper following these steps:
 
 1. module load conda/analysis3
 2. export PYTHONNOUSERSITE=1

requirements.txt

@@ -2,7 +2,8 @@
 # Optional dependencies e.g. [dev] are added in `test-requirements`
 click
 xarray>=2024.05.0
-cmor
+# tested to work with CMOR 3.11.0 
+cmor   
 numpy
 pyyaml
 dask

src/mopper/mop_setup.py

@@ -19,7 +19,7 @@
 # originally written for CMIP5 by Peter Uhe and dapted for CMIP6 by Chloe Mackallah
 # ( https://doi.org/10.5281/zenodo.7703469 )
 #
-# last updated 10/10/2024
+# last updated 01/08/2025
 
 import os
 import shutil
@@ -96,7 +96,10 @@ def find_matches(table, var, realm, frequency, mappings):
         resample = match.get('resample', '')
         timeshot, frequency, orig_timeshot = define_timeshot(frequency, resample,
             match['cell_methods'])
-        match['resample'] = f"{resample} {orig_timeshot}"
+        if resample != "":
+            resample = f"{resample} {orig_timeshot}"
+        match['resample'] = resample
+        mop_log.debug(f"Resample is {resample}")
         match['timeshot'] = timeshot
         match['table'] = table
         match['frequency'] = frequency