Rename package eturb -> snek5000

New subpackage: assets New module: output.base
snek5000 · May 8, 2020 · 9c7e201 · 9c7e201
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diff --git a/AUTHORS.md b/AUTHORS.md
@@ -1,4 +1,3 @@
 # Authors
 
 * [Ashwin Vishnu Mohanan](mailto:[email protected])
-* [Luigi Antonialli](mailto:[email protected])
diff --git a/CHANGELOG.md b/CHANGELOG.md
@@ -56,7 +56,7 @@ Security in case of vulnerabilities.
 
 ### Added
 - Tar shell functions in activate script
-- Module `eturb.clusters` for job submission
+- Module `snek5000.clusters` for job submission
 
 ### Changed
 - Conda environment packages
@@ -100,7 +100,7 @@ Security in case of vulnerabilities.
 ### Added
 - Uses `fluidsim` framework for creating a scripting layer
 - Package `abl` with a single module and an `abl.Output` class
-- New sub-packages and modules under `eturb`: `solvers, output, info, log,
+- New sub-packages and modules under `snek5000`: `solvers, output, info, log,
   make, magic, operators`
 - Testing with `pytest`, and CI on GitHub actions
 - Detailed documentation
@@ -114,6 +114,6 @@ Security in case of vulnerabilities.
 ## [0.0.1] - 2020-01-17
 
 ### Added
-- Scripting for managing run parameters `eturb.params`
+- Scripting for managing run parameters `snek5000.params`
 - Python packaging
 - Sphinx + Doxygen + Breathe documentation
diff --git a/CONTRIBUTING.md b/CONTRIBUTING.md
@@ -21,7 +21,7 @@ pip install -e '.[dev]'
   also rely on [git submodules](https://www.git-scm.com/docs/git-submodule) to
   track other libraries. The following branches are important:
 
-  * `eturb`:
+  * `snek5000`:
     * `master`: main branch
     * `develop`: development branch
   * `lib/Nek5000`:
@@ -40,7 +40,7 @@ pip install -e '.[dev]'
   top-level directory. The test-cases can be found under `tests/` directory.
 * **Debugging**: Set the environment variable:
   ```bash
-  export ETURB_DEBUG=true
+  export SNEK_DEBUG=true
   ```
   to activate debugging logs and longer tests.
 

diff --git a/README.md b/README.md
@@ -1,7 +1,7 @@
 # Project *eTurb*
 
-[![](https://github.com/exabl/eturb/workflows/Tests/badge.svg)](https://github.com/exabl/eturb/actions?workflow=Tests)
-[![](https://github.com/exabl/eturb/workflows/Docs/badge.svg)](https://github.com/exabl/eturb/actions?workflow=Docs)
+[![](https://github.com/exabl/snek5000/workflows/Tests/badge.svg)](https://github.com/exabl/snek5000/actions?workflow=Tests)
+[![](https://github.com/exabl/snek5000/workflows/Docs/badge.svg)](https://github.com/exabl/snek5000/actions?workflow=Docs)
 
 **Efficient** simulations of **turbulent** atmospheric boundary layer.
 
@@ -10,10 +10,10 @@
 
 ```sh
 # Clone
-git clone --recursive [email protected]:exabl/eturb.git
+git clone --recursive [email protected]:exabl/snek5000.git
 
 # Activate paths: Start here. Always!
-cd eturb
+cd snek5000
 source activate.sh
 
 # Build Nek5000
@@ -38,8 +38,8 @@ do this (and it has to be done only once):
    ```
 -  Using `conda`
    ```sh
-   conda env create -n eturb -f environment.yml
-   conda activate eturb
+   conda env create -n snek5000 -f environment.yml
+   conda activate snek5000
    pip install -e .
    ```
 After setting up Python, you can do either of the following:
@@ -60,11 +60,11 @@ After setting up Python, you can do either of the following:
    snakemake clean
    cd -
 
-2. Use the **[`eturb` Python
-   API](https://exabl.github.io/eturb/_generated/eturb.html)**, based on
+2. Use the **[`snek5000` Python
+   API](https://exabl.github.io/snek5000/_generated/snek5000.html)**, based on
    [fluidsim](https://fluidsim.readthedocs.io)
    ```python
-   from eturb.solvers.abl import Simul
+   from snek5000.solvers.abl import Simul
 
    params = Simul.create_default_params()
 

diff --git a/Snakefile b/Snakefile
@@ -1,5 +1,5 @@
 from glob import iglob
-from eturb.util.archive import tar_name, archive
+from snek5000.util.archive import tar_name, archive
 
 PYTHON_DIRECTORIES = ["docs", "src", "tests"]
 
@@ -9,7 +9,7 @@ rule env_export:
         """
         conda env export -f environment.yml
         sed -i '/^prefix/d' environment.yml
-        sed -i '/eturb/d' environment.yml
+        sed -i '/snek5000/d' environment.yml
         """
 
 rule env_update:
@@ -42,7 +42,7 @@ rule ctags:
     input:
         nek5000='lib/Nek5000/core',
         abl='src/abl',
-        eturb='src/eturb'
+        snek5000='src/snek5000'
     output:
         '.tags'
     params:
@@ -64,7 +64,7 @@ rule ctags:
         """
         ctags -f {output} --language-force=Fortran -R {input.nek5000}
         ctags -f {output} {params.excludes} --append --language-force=Fortran -R {input.abl}
-        ctags -f {output} {params.excludes} --append -R {input.eturb}
+        ctags -f {output} {params.excludes} --append -R {input.snek5000}
         """
 
 rule watch:

diff --git a/activate.sh b/activate.sh
@@ -25,9 +25,9 @@ function tar-diff() {
 
 if [ -d venv ]; then
   source venv/bin/activate
-elif [ -z "$CONDA_PREFIX" ]; then
+elif [[ -z "$CONDA_PREFIX" ]] && [[ -z "$VIRTUAL_ENV" ]]; then
   echo 'WARNING: no venv / conda environment present.'
-  echo 'Read the docs on how to setup your Python environment: https://exabl.github.io/eturb/README.html#easy-way'
+  echo 'Read the docs on how to setup your Python environment: https://exabl.github.io/snek5000/README.html#easy-way'
 fi
 
 if [ "$BASH_VERSION" ]; then

diff --git a/docs/Doxyfile b/docs/Doxyfile
@@ -790,7 +790,7 @@ WARN_LOGFILE           =
 # spaces. See also FILE_PATTERNS and EXTENSION_MAPPING
 # Note: If this tag is empty the current directory is searched.
 
-INPUT                  = .. ../lib/Nek5000/core ../src/abl ../src/abl/toolbox
+INPUT                  = .. ../lib/Nek5000/core
 
 # This tag can be used to specify the character encoding of the source files
 # that doxygen parses. Internally doxygen uses the UTF-8 encoding. Doxygen uses
@@ -859,57 +859,6 @@ FILE_PATTERNS          = *.c \
                          *.ucf \
                          *.qsf \
                          *.usr \
-                         ADJOINT \
-                         AVG \
-                         DEALIAS \
-                         DOMAIN \
-                         DXYZ \
-                         EIGEN \
-                         ESOLV \
-                         FDMH1 \
-                         GMRES \
-                         HSMG \
-                         IXYZ \
-                         MVGEOM \
-                         NEKUSE \
-                         NONCON \
-                         OPCTR \
-                         ORTHOP \
-                         ORTHOSTRS \
-                         ORTHOT \
-                         SCRCT \
-                         SEMHAT \
-                         STEADY \
-                         TOPOL \
-                         VPROJ \
-                         WZ \
-                         WZF \
-                         CTIMER \
-                         CVODE \
-                         GEOM \
-                         GFLDR \
-                         GLOBALCOM \
-                         HEADER \
-                         INPUT \
-                         MASS \
-                         NEKNEK \
-                         PARALLEL \
-                         PARDICT \
-                         RESTART \
-                         SOLN \
-                         TOTAL \
-                         TSTEP \
-                         ZPER \
-                         SIZE \
-                         CHKPOINTD \
-                         CHKPTMSTPD \
-                         FRAMELP \
-                         IOTOOLD \
-                         MAP2D \
-                         MNTRLOGD \
-                         MNTRTMRD \
-                         RPRMD \
-                         STATD
                          # *.py \
 
 # The RECURSIVE tag can be used to specify whether or not subdirectories should

diff --git a/docs/abl.rst b/docs/abl.rst
diff --git a/docs/conf.py b/docs/conf.py
@@ -22,9 +22,7 @@
 from subprocess import PIPE
 
 import breathe
-
-import abl
-import eturb
+import snek5000
 
 
 def root(module):
@@ -36,23 +34,22 @@ def root(module):
 # If extensions (or modules to document with autodoc) are in another directory,
 # add these directories to sys.path here. If the directory is relative to the
 # documentation root, use os.path.abspath to make it absolute, like shown here.
-sys.path.insert(0, root(abl))
-sys.path.insert(0, root(eturb))
+sys.path.insert(0, root(snek5000))
 
 print("sys.path =\n   ", "\n    ".join(sys.path))
 
 # -- Project information -----------------------------------------------------
 
-project = "eturb"
+project = "snek5000"
 _today = date.today()
 copyright = (
     f"2019 - {_today.year}, Ashwin Vishnu Mohanan. Published: {_today.isoformat()}"
 )
 author = "Ashwin Vishnu Mohanan"
 
-version = ".".join(eturb.__version__.split(".")[:3])
+version = ".".join(snek5000.__version__.split(".")[:3])
 # The full version, including alpha/beta/rc tags
-release = eturb.__version__
+release = snek5000.__version__
 
 
 # -- General configuration ---------------------------------------------------
@@ -74,10 +71,7 @@ def root(module):
 os.makedirs("_build/html/doxygen", exist_ok=True)
 
 # Inspect whether to run doxygen or not
-last_modified = max(
-    eturb.util.last_modified("../lib").stat().st_mtime,
-    eturb.util.last_modified("../src/abl").stat().st_mtime,
-)
+last_modified = snek5000.util.last_modified("../lib").stat().st_mtime
 timestamp = Path("_build/.doxygen_timestamp")
 if timestamp.exists() and Path("_build/xml").exists():
     with open(timestamp) as fp:
@@ -132,11 +126,11 @@ def root(module):
     breathe_domain_by_file_pattern = {"SIZE": "f"}
 
     # Input sources
-    breathe_projects = {"eturb": "_build/xml/"}
+    breathe_projects = {"snek5000": "_build/xml/"}
     #  breathe_projects_source = {
     #      "abl": ("../src/abl", ["SIZE", "abl.usr"]),
     #  }
-    breathe_default_project = "eturb"
+    breathe_default_project = "snek5000"
 
 # ----------------------------------------------------------------------------
 

diff --git a/docs/index.rst b/docs/index.rst
@@ -1,4 +1,4 @@
-.. eturb documentation master file, created by
+.. snek5000 documentation master file, created by
    sphinx-quickstart on Wed Dec 25 01:55:26 2019.
    You can adapt this file completely to your liking, but it should at least
    contain the root `toctree` directive.
@@ -16,11 +16,11 @@ Welcome to project *eTurb*'s documentation!
    -->
    <img style="float: right;" src="_static/icon.svg" width="100rem"/>
 
-+------------+--------------------------------+
-| Repository | https://github.com/exabl/eturb |
-+------------+--------------------------------+
-| Version    | |release|                      |
-+------------+--------------------------------+
++------------+-----------------------------------+
+| Repository | https://github.com/exabl/snek5000 |
++------------+-----------------------------------+
+| Version    | |release|                         |
++------------+-----------------------------------+
 
 .. toctree::
    :maxdepth: 2
@@ -32,14 +32,12 @@ Welcome to project *eTurb*'s documentation!
    :maxdepth: 2
    :caption: User Guide
 
-   abl
    nek5000
 
 .. autosummary::
    :toctree: _generated/
 
-   eturb
-   abl
+   snek5000
 
 .. toctree::
    :maxdepth: 1

diff --git a/docs/nek5000.rst b/docs/nek5000.rst
@@ -4,10 +4,8 @@ Nek5000 core library
 .. note::
 
     The following is auto-generated using Doxygen and represents a fork_ of
-    Nek5000 v17. Only subroutines relevant to eturb project are listed here.
+    Nek5000 v17. Only subroutines relevant to snek5000 project are listed here.
     The `official documentation`_ is hand-written and is more general.
 
-.. doxygengroup:: core
-
 .. _fork: https://github.com/exabl/Nek5000
 .. _official documentation: https://nek5000.github.io/NekDoc/appendix.html
diff --git a/pyproject.toml b/pyproject.toml
@@ -3,5 +3,5 @@ requires = ["setuptools>=42.0.0", "wheel", "setuptools_scm[toml]>=3.4.2"]
 
 
 [tool.setuptools_scm]
-write_to = "src/eturb/_version.py"
+write_to = "src/snek5000/_version.py"
 write_to_template = "__version__ = \"{version}\"\n"
diff --git a/setup.cfg b/setup.cfg
@@ -1,9 +1,9 @@
 [metadata]
 author = Ashwin Vishnu Mohanan
 author_email = [email protected]
-url = https://exabl.github.io/eturb
-name = eturb
-description = Python utilities for eturb project
+url = https://github.com/exabl/snek5000-abl
+name = abl
+description = Python utilities for snek5000 project
 long_description = file: README.md, HISTORY.md
 long_description_content_type = text/markdown
 license = BSD-3-Clause
@@ -65,5 +65,5 @@ ignore = E501,W503,W505
 max-line-lenght = 82
 
 [isort]
-known_first_party = fluiddyn, fluidsim, eturb, abl
+known_first_party = fluiddyn, fluidsim, snek5000, abl
 multi_line_output = 3