Merge pull request #10 from snek5000/prepare-0.4.0

Prepare 0.4.0
snek5000 · Dec 6, 2022 · ea28d3e · ea28d3e
2 parents e59c371 + 07722a1
commit ea28d3e
Show file tree

Hide file tree

Showing 19 changed files with 75 additions and 40 deletions.
diff --git a/.pre-commit-config.yaml b/.pre-commit-config.yaml
@@ -0,0 +1,35 @@
+# See https://pre-commit.com for more information
+# See https://pre-commit.com/hooks.html for more hooks
+repos:
+- repo: https://github.com/pre-commit/pre-commit-hooks
+  rev: v4.4.0
+  hooks:
+  - id: check-toml
+  - id: check-yaml
+  - id: end-of-file-fixer
+  - id: check-added-large-files
+
+- repo: https://github.com/psf/black
+  rev: 22.10.0
+  hooks:
+  - id: black
+- repo: https://github.com/PyCQA/isort
+  rev: 5.10.1
+  hooks:
+  - id: isort
+- repo: https://github.com/PyCQA/flake8
+  rev: 6.0.0
+  hooks:
+  - id: flake8
+- repo: https://github.com/snakemake/snakefmt
+  rev: v0.7.0
+  hooks:
+  - id: snakefmt
+- repo: https://github.com/executablebooks/mdformat
+  rev: 0.7.16
+  hooks:
+  - id: mdformat
+    additional_dependencies:
+    - mdformat-tables
+    - mdformat-frontmatter
+    - mdformat-myst
diff --git a/README.md b/README.md
@@ -1,16 +1,24 @@
 # snek5000-phill
 
-Nek5000 [phill
-example](https://github.com/KTH-Nek5000/KTH_Examples/tree/master/phill_STAT)
-executed via [snek5000](https://github.com/exabl/snek5000).
+The [Nek5000 phill example] adapted for a workflow using [Snek5000].
 
+## Install
 
-## Quick start
+```sh
+pip install snek5000-phill
+```
+
+For more details, see https://snek5000.readthedocs.io/en/latest/install.html.
+
+## Tests
 
 ```sh
-pip install -e '.[tests]'
+pip install '.[tests]'
 # Run simple tests: including compilation
 pytest
 # Run slow tests: launches simulation
 pytest --runslow
 ```
+
+[nek5000 phill example]: https://github.com/KTH-Nek5000/KTH_Examples/tree/master/phill_STAT
+[snek5000]: https://github.com/exabl/snek5000
diff --git a/setup.cfg b/setup.cfg
@@ -19,7 +19,7 @@ package_dir=
     =src
 packages=find:
 install_requires =
-    snek5000 >= 0.7.0b0
+    snek5000 >= 0.8.0rc1
 setup_requires =
     setuptools_scm
 

diff --git a/src/phill/Snakefile b/src/phill/Snakefile
@@ -4,6 +4,7 @@ from phill import short_name, Output
 
 configfile: "config_simul.yml"
 
+
 ensure_env()
 
 # Necessary to pass configuration to other Snakemake modules

diff --git a/src/phill/__init__.py b/src/phill/__init__.py
@@ -13,10 +13,8 @@
 
 """
 from ._version import __version__  # noqa: F401
-
-from .solver import Simul
 from .output import Output
-
+from .solver import Simul
 
 short_name = "phill"
 __all__ = ["Simul", "Output", "short_name"]
diff --git a/src/phill/etc/tetralith.yml b/src/phill/etc/tetralith.yml
@@ -5,4 +5,3 @@ MPIFC: mpiifort
 MPIEXEC: "mpiexec"
 CFLAGS: "-march=native"
 FFLAGS: "-march=native -mcmodel=medium"
-
diff --git a/src/phill/output.py b/src/phill/output.py
@@ -1,10 +1,9 @@
+from phill.templates import box, makefile_usr, size
 from snek5000 import mpi
 from snek5000.output.base import Output as OutputBase
-from phill.templates import box, size, makefile_usr
 
 
 class OutputPhill(OutputBase):
-
     @property
     def makefile_usr_sources(self):
         """

diff --git a/src/phill/phill.usr b/src/phill/phill.usr
@@ -619,4 +619,3 @@ c-----------------------------------------------------------------------
       end subroutine
 !======================================================================
 ! vim: set ft=fortran
-
diff --git a/src/phill/solver.py b/src/phill/solver.py
@@ -27,9 +27,8 @@ def _init_root(self):
 
 
 class SimulPhill(SimulKTH):
-    """A solver which compiles and runs using a Snakefile.
+    """A solver which compiles and runs using a Snakefile."""
 
-    """
     InfoSolver = InfoSolverPhill
 
     @classmethod
@@ -63,13 +62,13 @@ def create_default_params(cls):
         general.stop_at = "num_steps"
         general.num_steps = 20
         general.dt = -2e-4
-        general.time_stepper = 'bdf3'
+        general.time_stepper = "bdf3"
         general.variable_dt = False
         general.target_cfl = 0.3
-        general.write_control = 'timestep'
+        general.write_control = "timestep"
         general.write_interval = 100
         general.dealiasing = True
-        general.filtering = 'explicit'
+        general.filtering = "explicit"
         general.filter_weight = 0.02
         general.filter_cutoff_ratio = 0.67
 
@@ -78,7 +77,7 @@ def create_default_params(cls):
 
         params.nek.pressure.residual_tol = params.nek.velocity.residual_tol = 1e-8
         params.nek.pressure.residual_proj = params.nek.velocity.residual_proj = 1e-8
-        params.nek.velocity.density = 1.
+        params.nek.velocity.density = 1.0
         params.nek.velocity.viscosity = -700
 
         # User parameters for KTH framework
@@ -97,8 +96,8 @@ def create_default_params(cls):
         oper.ny = 16
         oper.nz = 19
 
-        oper.Lx = oper.Ly = oper.Lz = 1.
-        oper.boundary = ['P', 'P', 'W', 'W', 'P', 'P']
+        oper.Lx = oper.Ly = oper.Lz = 1.0
+        oper.boundary = ["P", "P", "W", "W", "P", "P"]
 
         # Set SIZE file parameters
         # ------------------------

diff --git a/src/phill/toolbox/CHKPOINTD b/src/phill/toolbox/CHKPOINTD
@@ -52,4 +52,4 @@
      $  chpt_step, chpt_step_id, chpt_set_o, chpt_set_i, 
      $  chpt_reset, chpt_stepc, chpt_istep, chpt_nstep
 
-      common /CHKPNTL/ chpt_ifinit, chpt_ifrst
+      common /CHKPNTL/ chpt_ifinit, chpt_ifrst
diff --git a/src/phill/toolbox/FRAMELP b/src/phill/toolbox/FRAMELP
@@ -27,4 +27,4 @@
       integer rpar_log ! logical vriable
       parameter (rpar_log=3)
       integer rpar_str ! string vriable
-      parameter (rpar_str=4)
+      parameter (rpar_str=4)
diff --git a/src/phill/toolbox/IOTOOLD b/src/phill/toolbox/IOTOOLD
@@ -15,4 +15,4 @@
       !     common blocks
       common /iotooli/ io_id
 
-      common /io_iunit/ io_iunit_min, io_iunit_max
+      common /io_iunit/ io_iunit_min, io_iunit_max
diff --git a/src/phill/toolbox/MNTRLOGD b/src/phill/toolbox/MNTRLOGD
@@ -89,4 +89,4 @@
 
 !     string variables
       common /MNTRLOGC/ mntr_wtimes, mntr_mod_name, mntr_mod_dscr
-
+
diff --git a/src/phill/toolbox/MNTRTMRD b/src/phill/toolbox/MNTRTMRD
@@ -38,4 +38,4 @@
       common /MNTRTMRL/ mntr_tmr_sum
 
       common /MNTRTMRC/ mntr_tmr_name, mntr_tmr_dscr
-
+
diff --git a/src/phill/toolbox/README.md b/src/phill/toolbox/README.md
@@ -3,12 +3,13 @@
 This directory contains the [turbulence statistics tools](https://github.com/KTH-Nek5000/KTH_Toolbox/).
 
 ## Tool list:
-* [frame](https://kth-nek5000.github.io/KTH_Framework/group__frame.html) - backbone of the toolbox
-* [monitor](https://kth-nek5000.github.io/KTH_Framework/group__monitor.html) - monitoring tool: logging and timing
-* [runparam](https://kth-nek5000.github.io/KTH_Framework/group__runparam.html) - runtime parameters
-* [io_tool](https://kth-nek5000.github.io/KTH_Framework/group__io__tools.html) - simple I/O tools
-* [checkpoint](https://kth-nek5000.github.io/KTH_Framework/group__chkpoint.html) - checkpointing main interface
-* [mstep](https://kth-nek5000.github.io/KTH_Framework/group__chkpoint__mstep.html) - multi-step checkpointing
-* [math](https://kth-nek5000.github.io/KTH_Framework/group__math.html) - simple math tools
-* [map2D] - 3D to 2D grid mapping for 2D-extruded meshes
-* [stat] - turbulence statistics tool
+
+- [frame](https://kth-nek5000.github.io/KTH_Framework/group__frame.html) - backbone of the toolbox
+- [monitor](https://kth-nek5000.github.io/KTH_Framework/group__monitor.html) - monitoring tool: logging and timing
+- [runparam](https://kth-nek5000.github.io/KTH_Framework/group__runparam.html) - runtime parameters
+- [io_tool](https://kth-nek5000.github.io/KTH_Framework/group__io__tools.html) - simple I/O tools
+- [checkpoint](https://kth-nek5000.github.io/KTH_Framework/group__chkpoint.html) - checkpointing main interface
+- [mstep](https://kth-nek5000.github.io/KTH_Framework/group__chkpoint__mstep.html) - multi-step checkpointing
+- [math](https://kth-nek5000.github.io/KTH_Framework/group__math.html) - simple math tools
+- \[map2D\] - 3D to 2D grid mapping for 2D-extruded meshes
+- \[stat\] - turbulence statistics tool
diff --git a/src/phill/toolbox/RPRMD b/src/phill/toolbox/RPRMD
@@ -87,4 +87,4 @@
 !     string variables
       common /RPRMC/ rprm_parfnm, rprm_sec_name, rprm_sec_dscr, 
      $       rprm_par_name, rprm_par_dscr, rprm_parv_str
-
+
diff --git a/src/phill/toolbox/frame.f b/src/phill/toolbox/frame.f
@@ -103,5 +103,3 @@ integer function frame_get_master()
       return
       end function
 !=======================================================================
-
-
diff --git a/src/phill/toolbox/mntrtmr.f b/src/phill/toolbox/mntrtmr.f
@@ -459,4 +459,3 @@ subroutine mntr_tmr_get_olist(olist,ierr)
       return
       end subroutine
 !=======================================================================
-
diff --git a/src/phill/toolbox/stat_IO.f b/src/phill/toolbox/stat_IO.f
@@ -751,4 +751,3 @@ subroutine stat_mfo_crd2D
       return
       end subroutine
 !=======================================================================
-