Merge pull request #232 from snek5000/fix-non-editable-install

Try to use non editable installations.

CHANGELOG.md

@@ -85,6 +85,8 @@ deprecations.
 
 ### Deprecated
 
+- {func}`snek5000.params._complete_params_from_par_file` (renamed as
+  {func}`snek5000.params.complete_params_from_par_file`).
 - {func}`snek5000.util.restart.prepare_for_restart`
 - Passing rules as iterables to {meth}`snek5000.make.Make.exec`. Pass positional
   parameters instead.

docs/conf.py

@@ -87,6 +87,7 @@ def root(module):
     "sphinx.ext.todo",
     "sphinx.ext.viewcode",
     "sphinx_inline_tabs",
+    "IPython.sphinxext.ipython_console_highlighting",
     #  "recommonmark",
     #  "myst_parser",
     "myst_nb",

docs/dev/params.rst

@@ -28,7 +28,6 @@ Inspection
 Input / Output
 --------------
 
-.. autofunction:: snek5000.params._complete_params_from_par_file
 .. autofunction:: snek5000.params._complete_params_from_xml_file
 .. autofunction:: snek5000.params._save_recorded_user_params
 .. autofunction:: snek5000.params._load_recorded_user_params

docs/examples/snek5000-canonical/setup.cfg

@@ -22,4 +22,4 @@ snek5000.solvers =
 where=src
 
 [options.package_data]
-snek5000_canonical = templates/*.j2, *.usr.f, Snakefile, etc/*.yml
+snek5000_canonical = templates/*.j2, *.usr.f, *.par.cfg, Snakefile, etc/*.yml

docs/examples/snek5000-tgv/setup.cfg

@@ -22,4 +22,4 @@ snek5000.solvers =
 where=src
 
 [options.package_data]
-snek5000_tgv = templates/*.j2, *.usr.f, Snakefile, etc/*.yml
+snek5000_tgv = templates/*.j2, *.usr.f, *.par.cfg, Snakefile, etc/*.yml

docs/examples/snek5000-tgv/src/snek5000_tgv/solver.py

@@ -1,7 +1,7 @@
 from math import pi
 
 from snek5000.info import InfoSolverMake
-from snek5000.params import _complete_params_from_par_file
+from snek5000.params import complete_params_from_par_file
 from snek5000.solvers.base import SimulNek
 
 
@@ -49,7 +49,7 @@ def create_default_params(cls):
         info_solver = cls.info_solver  # cls.InfoSolver()
         output_cls = info_solver.import_classes()["Output"]
         root = output_cls.get_root()
-        _complete_params_from_par_file(
+        complete_params_from_par_file(
             params, root / f"{info_solver.short_name}.par.cfg"
         )
 

docs/tuto_phill_setup.md

@@ -24,7 +24,7 @@ looks like. To get started, we install everything we need:
 ```sh
 python -m venv venv
 source venv/bin/activate
-pip install -e "snek5000-phill @ git+https://github.com/snek5000/snek5000-phill.git"
+pip install "snek5000-phill @ git+https://github.com/snek5000/snek5000-phill.git"
 ```
 
 ```{note}

noxfile.py

@@ -154,6 +154,11 @@ def pip_compile(session, extra):
     session.log(f"Removing absolute paths from {out_file}")
     packages = out_file.read_text()
     rel_path_packages = packages.replace("file://" + str(Path.cwd().resolve()), ".")
+
+    # special cases for snek5000-canonical and snek5000-tgv
+    for package in ("snek5000-canonical", "snek5000-tgv"):
+        rel_path_packages = rel_path_packages.replace(f"{package} @ ", "")
+
     if extra == "tests":
         tests_editable = out_file.parent / out_file.name.replace(
             "tests", "tests-editable"

requirements/dev.txt

@@ -1,6 +1,6 @@
 #
-# This file is autogenerated by pip-compile with python 3.9
-# To update, run:
+# This file is autogenerated by pip-compile with Python 3.9
+# by the following command:
 #
 #    pip-compile --extra=dev --output-file=requirements/dev.txt --resolver=backtracking requirements/vcs_packages.in setup.cfg
 #
@@ -11,10 +11,6 @@
     #   snek5000-cbox
     #   snek5000-phill
     #   snek5000-tgv
--e ./docs/examples/snek5000-canonical
-    # via -r requirements/vcs_packages.in
--e ./docs/examples/snek5000-tgv
-    # via -r requirements/vcs_packages.in
 alabaster==0.7.12
     # via sphinx
 anyio==3.6.2
@@ -27,7 +23,7 @@ argon2-cffi==21.3.0
     # via jupyter-server
 argon2-cffi-bindings==21.2.0
     # via argon2-cffi
-asttokens==2.1.0
+asttokens==2.2.1
     # via stack-data
 attrs==22.1.0
     # via
@@ -83,13 +79,13 @@ coverage[toml]==6.5.0
     # via
     #   pytest-cov
     #   snek5000 (setup.cfg)
-cryptography==38.0.3
+cryptography==38.0.4
     # via secretstorage
 cycler==0.11.0
     # via matplotlib
 datrie==0.8.2
     # via snakemake
-debugpy==1.6.3
+debugpy==1.6.4
     # via ipykernel
 decorator==5.1.1
     # via ipython
@@ -99,7 +95,7 @@ distlib==0.3.6
     # via virtualenv
 distro==1.8.0
     # via fluiddyn
-docstring-to-markdown==0.10
+docstring-to-markdown==0.11
     # via python-lsp-server
 docutils==0.17.1
     # via
@@ -109,19 +105,19 @@ docutils==0.17.1
     #   snakemake
     #   snek5000 (setup.cfg)
     #   sphinx
-dpath==2.0.6
+dpath==2.1.2
     # via yte
 entrypoints==0.4
     # via jupyter-client
-exceptiongroup==1.0.1
+exceptiongroup==1.0.4
     # via pytest
 executing==1.2.0
     # via stack-data
 fancycompleter==0.9.1
     # via pdbpp
 fastjsonschema==2.16.2
     # via nbformat
-filelock==3.8.0
+filelock==3.8.1
     # via
     #   snek5000
     #   snek5000 (setup.cfg)
@@ -141,29 +137,29 @@ fortran-language-server==1.12.0
     # via snek5000 (setup.cfg)
 furo==2022.9.29
     # via snek5000 (setup.cfg)
-gitdb==4.0.9
+gitdb==4.0.10
     # via gitpython
 gitpython==3.1.29
     # via
     #   nbdime
     #   snakemake
 greenlet==2.0.1
     # via sqlalchemy
-h5netcdf==1.0.2
+h5netcdf==1.1.0
     # via fluiddyn
 h5py==3.7.0
     # via
     #   fluiddyn
     #   h5netcdf
-identify==2.5.8
+identify==2.5.9
     # via pre-commit
 idna==3.4
     # via
     #   anyio
     #   requests
 imagesize==1.4.1
     # via sphinx
-importlib-metadata==5.0.0
+importlib-metadata==5.1.0
     # via
     #   fluidsim-core
     #   jupyter-cache
@@ -180,14 +176,14 @@ iniconfig==1.1.1
     # via pytest
 ipykernel==6.17.1
     # via myst-nb
-ipython==8.6.0
+ipython==8.7.0
     # via
     #   ipykernel
     #   myst-nb
     #   snek5000 (setup.cfg)
 jaraco-classes==3.2.3
     # via keyring
-jedi==0.18.1
+jedi==0.18.2
     # via
     #   ipython
     #   python-lsp-server
@@ -205,24 +201,24 @@ jinja2==3.1.2
     #   snek5000
     #   snek5000 (setup.cfg)
     #   sphinx
-jsonschema==4.17.0
+jsonschema==4.17.3
     # via
     #   nbformat
     #   snakemake
 jupyter-cache==0.5.0
     # via myst-nb
-jupyter-client==7.4.5
+jupyter-client==7.4.7
     # via
     #   ipykernel
     #   jupyter-server
     #   nbclient
-jupyter-core==5.0.0
+jupyter-core==5.1.0
     # via
     #   jupyter-client
     #   jupyter-server
     #   nbconvert
     #   nbformat
-jupyter-server==1.23.1
+jupyter-server==1.23.3
     # via
     #   jupyter-server-mathjax
     #   nbdime
@@ -271,7 +267,7 @@ nbclient==0.5.13
     #   jupyter-cache
     #   myst-nb
     #   nbconvert
-nbconvert==7.2.4
+nbconvert==7.2.5
     # via jupyter-server
 nbdime==3.1.1
     # via snek5000 (setup.cfg)
@@ -291,9 +287,9 @@ nest-asyncio==1.5.6
     #   nbclient
 nodeenv==1.7.0
     # via pre-commit
-nox==2022.8.7
+nox==2022.11.21
     # via snek5000 (setup.cfg)
-numpy==1.23.4
+numpy==1.23.5
     # via
     #   contourpy
     #   fluiddyn
@@ -317,7 +313,7 @@ packaging==21.3
     #   setuptools-scm
     #   sphinx
     #   xarray
-pandas==1.5.1
+pandas==1.5.2
     # via
     #   snek5000
     #   snek5000 (setup.cfg)
@@ -336,11 +332,11 @@ pickleshare==0.7.5
     # via ipython
 pillow==9.3.0
     # via matplotlib
-pkginfo==1.8.3
+pkginfo==1.9.2
     # via twine
 plac==1.3.5
     # via yte
-platformdirs==2.5.3
+platformdirs==2.5.4
     # via
     #   jupyter-core
     #   virtualenv
@@ -352,7 +348,7 @@ pre-commit==2.20.0
     # via snek5000 (setup.cfg)
 prometheus-client==0.15.0
     # via jupyter-server
-prompt-toolkit==3.0.32
+prompt-toolkit==3.0.33
     # via ipython
 psutil==5.9.4
     # via
@@ -367,8 +363,6 @@ pulp==2.7.0
     # via snakemake
 pure-eval==0.2.2
     # via stack-data
-py==1.11.0
-    # via nox
 pycparser==2.21
     # via cffi
 pygments==2.13.0
@@ -477,10 +471,14 @@ snakemake==7.18.2
     # via
     #   snek5000
     #   snek5000 (setup.cfg)
+./docs/examples/snek5000-canonical
+    # via -r requirements/vcs_packages.in
 snek5000-cbox @ git+https://github.com/snek5000/snek5000-cbox.git
     # via -r requirements/vcs_packages.in
 snek5000-phill @ git+https://github.com/snek5000/snek5000-phill.git
     # via -r requirements/vcs_packages.in
+./docs/examples/snek5000-tgv
+    # via -r requirements/vcs_packages.in
 sniffio==1.3.0
     # via anyio
 snowballstemmer==2.2.0
@@ -502,7 +500,7 @@ sphinx-autobuild==2021.3.14
     # via snek5000 (setup.cfg)
 sphinx-basic-ng==1.0.0b1
     # via furo
-sphinx-copybutton==0.5.0
+sphinx-copybutton==0.5.1
     # via snek5000 (setup.cfg)
 sphinx-inline-tabs==2022.1.2b11
     # via snek5000 (setup.cfg)
@@ -518,9 +516,9 @@ sphinxcontrib-qthelp==1.0.3
     # via sphinx
 sphinxcontrib-serializinghtml==1.1.5
     # via sphinx
-sqlalchemy==1.4.43
+sqlalchemy==1.4.44
     # via jupyter-cache
-stack-data==0.6.0
+stack-data==0.6.2
     # via ipython
 stopit==1.1.2
     # via snakemake
@@ -530,7 +528,7 @@ tabulate==0.9.0
     #   snakemake
 terminado==0.17.0
     # via jupyter-server
-throttler==1.2.1
+throttler==1.2.2
     # via snakemake
 tinycss2==1.2.1
     # via nbconvert
@@ -553,7 +551,7 @@ tornado==6.2
     #   livereload
     #   nbdime
     #   terminado
-traitlets==5.5.0
+traitlets==5.6.0
     # via
     #   ipykernel
     #   ipython
@@ -564,7 +562,7 @@ traitlets==5.5.0
     #   nbclient
     #   nbconvert
     #   nbformat
-twine==4.0.1
+twine==4.0.2
     # via snek5000 (setup.cfg)
 typing-extensions==4.4.0
     # via
@@ -573,15 +571,15 @@ typing-extensions==4.4.0
     #   setuptools-scm
 uc-micro-py==1.0.1
     # via linkify-it-py
-ujson==5.5.0
+ujson==5.6.0
     # via
     #   python-lsp-jsonrpc
     #   python-lsp-server
-urllib3==1.26.12
+urllib3==1.26.13
     # via
     #   requests
     #   twine
-virtualenv==20.16.6
+virtualenv==20.17.0
     # via
     #   nox
     #   pre-commit
@@ -597,11 +595,11 @@ wmctrl==0.4
     # via pdbpp
 wrapt==1.14.1
     # via snakemake
-xarray==2022.11.0
+xarray==2022.12.0
     # via pymech
 yte==1.5.1
     # via snakemake
-zipp==3.10.0
+zipp==3.11.0
     # via importlib-metadata
 
 # The following packages are considered to be unsafe in a requirements file: