Pin python version and environment

.github/workflows/pre-commit.yml

@@ -19,16 +19,16 @@ jobs:
     - name: Set up Python
       uses: actions/setup-python@v2
       with:
-        python-version: 3.11.0
+        python-version: 3.10.8
     - uses: conda-incubator/setup-miniconda@v2
       with:
         miniconda-version: "latest"
         channels: conda-forge
         channel-priority: flexible
         show-channel-urls: true
-    - name: Create env from unpinned reqs
+    - name: Create env from pinned environment
       run: |
-        conda env create --name dev_env --file requirements/requirements.yml
+        conda env create --name dev_env --file requirements/environment.yml
     - name: Install pre-commit hooks
       run: |
         conda run --name dev_env pre-commit install-hooks

.github/workflows/pytest.yml

@@ -19,18 +19,18 @@ jobs:
     - name: Set up Python
       uses: actions/setup-python@v2
       with:
-        python-version: 3.11.0
+        python-version: 3.10.8
     - uses: conda-incubator/setup-miniconda@v2
       with:
         miniconda-version: "latest"
         channels: conda-forge
         channel-priority: flexible
         show-channel-urls: true
-    - name: Create dev env from unpinned reqs
+    - name: Create env from pinned environment
       run: |
-        conda env create --name dev_env --file requirements/requirements.yml
+        ./setup_env.sh -n probtest
     - name: Run Pytest
       env:
         TZ: Europe/Zurich
       run: |
-        conda run --name dev_env pytest -v -s --cov --cov-report=term tests/
+        conda run --name probtest pytest -v -s --cov --cov-report=term tests/

.gitignore

@@ -1,6 +1,5 @@
 .idea*
-.vscode/*
-!.vscode/settings.json
+.vscode
 *pycache*
 *.swp
 *.pdf
@@ -9,6 +8,7 @@
 *.nc
 .coverage
 coverage.xml
+miniconda
 
 # output from unittest
 test_stats.csv

README.md

@@ -107,7 +107,8 @@ setup scripts:
 
 ```console
 ./setup_miniconda.sh
-./setup_env.sh -n probtest -u
+source miniconda/bin/activate
+./setup_env.sh
 ```
 
 #### Initialize probtest

engine/cdo_table.py

@@ -45,7 +45,7 @@ def rel_diff_stats(
     horizontal_dims,
     xarray_ds,
     fill_value_key,
-):  # pylint: disable=unused-argument
+):  # pylint: disable=unused-argument, too-many-positional-arguments
     dims = xarray_ds[varname].dims
     dataarray = xarray_ds[varname]
     time = xarray_ds[time_dim].values
@@ -125,7 +125,7 @@ def cdo_table(
     perturbed_model_output_dir,
     cdo_table_file,
     file_specification,
-):
+):  # pylint: disable=too-many-positional-arguments
     # TODO: A single perturbed run provides enough data to make proper statistics.
     #       refactor cdo_table interface to reflect that
     if len(member_num) == 1:

engine/init.py

@@ -96,7 +96,7 @@ def init(
     timing_current,
     timing_reference,
     append_time,
-):
+):  # pylint: disable=too-many-positional-arguments
     template_partition = str(template_name).rpartition("/")
     env = Environment(
         loader=FileSystemLoader(template_partition[0]), undefined=StrictUndefined

engine/performance_check.py

@@ -50,7 +50,7 @@ def performance_check(
     measurement_uncertainty,
     tolerance_factor,
     new_reference_threshold,
-):
+):  # pylint: disable=too-many-positional-arguments
     ttcur = TimingTree.from_json(timing_current)
     ttref = TimingTree.from_json(timing_reference)
 

engine/perturb.py

@@ -100,7 +100,7 @@ def perturb(
     variable_names,
     perturb_amplitude,
     copy_all_files,
-):  # pylint: disable=unused-argument
+):  # pylint: disable=unused-argument, too-many-positional-arguments
 
     processed_member_num = process_member_num(member_num)
 

engine/run_ensemble.py

@@ -71,7 +71,7 @@ def prepare_perturbed_run_script(
     rhs_new,
     rhs_old,
     seed,
-):
+):  # pylint: disable=too-many-positional-arguments
     with open(runscript, "r", encoding="utf-8") as in_file:
         with open(perturbed_runscript, "w", encoding="utf-8") as out_file:
 
@@ -222,7 +222,7 @@ def run_ensemble(
     lhs,
     rhs_new,
     rhs_old,
-):
+):  # pylint: disable=too-many-positional-arguments
     perturbed_run_dir = perturbed_run_dir if perturbed_run_dir else run_dir
     os.chdir(run_dir)
     job_list = []

engine/select_members.py

@@ -33,7 +33,7 @@ def find_members_and_factor_validating_for_all_stats_files(
     min_factor,
     max_factor,
     iterations,
-):
+):  # pylint: disable=too-many-positional-arguments
 
     members = list(range(1, total_member_num + 1))
 
@@ -263,7 +263,7 @@ def select_members(
     min_factor,
     max_factor,
     iterations,
-):  # pylint: disable=unused-argument
+):  # pylint: disable=unused-argument, too-many-positional-arguments
 
     if min_member_num > max_member_num:
         logger.error(

engine/stats.py

@@ -41,7 +41,7 @@ def process_member(
     file_id,
     stats_file_name,
     file_specification,
-):
+):  # pylint: disable=too-many-positional-arguments
     if m_num == 0:
         input_dir = model_output_dir
         m_id = "ref"
@@ -110,7 +110,7 @@ def stats(
     member_type,
     perturbed_model_output_dir,
     file_specification,
-):
+):  # pylint: disable=too-many-positional-arguments
     file_specification = file_specification[0]  # can't store dicts as defaults in click
     assert isinstance(file_specification, dict), "must be dict"