Renaming for new package (#17)

resmda->dageo; ES-MDA->ESMDA; m->z

.github/workflows/linux.yml

@@ -80,13 +80,13 @@ jobs:
 
       - name: Flake8
         shell: bash -l {0}
-        run: flake8 docs/conf.py resmda/ tests/
+        run: flake8 docs/conf.py dageo/ tests/
 
       - name: Test with pytest
         shell: bash -l {0}
         run: |
           python -m pip install .
-          pytest --cov=resmda
+          pytest --cov=dageo
 
   deploy:
     needs: test

.gitignore

@@ -3,7 +3,7 @@ __pycache__/
 
 # Sphinx
 docs/_build/
-docs/api/resmda*
+docs/api/dageo*
 docs/savefig/
 docs/gallery/*
 docs/sg_execution_times.rst
@@ -15,10 +15,10 @@ htmlcov
 .pytest_cache/
 
 # setuptools_scm
-resmda/version.py
+dageo/version.py
 
 # Build related
 .eggs/
 build/
 dist/
-resmda.egg-info/
+dageo.egg-info/

Makefile

@@ -22,11 +22,11 @@ dev-install:
 .ONESHELL:
 pytest:
 	rm -rf .coverage htmlcov/ .pytest_cache/
-	pytest --cov=resmda
+	pytest --cov=dageo
 	coverage html
 
 flake8:
-	flake8 docs/conf.py resmda/ tests/ examples/
+	flake8 docs/conf.py dageo/ tests/ examples/
 
 html:
 	cd docs && make html
@@ -35,7 +35,7 @@ html-noplot:
 	cd docs && make html-noplot
 
 html-clean:
-	cd docs && rm -rf api/resmda* gallery/* _build/ && make html
+	cd docs && rm -rf api/dageo* gallery/* _build/ && make html
 
 preview:
 	xdg-open docs/_build/html/index.html
@@ -44,9 +44,9 @@ linkcheck:
 	cd docs && make linkcheck
 
 clean:
-	python -m pip uninstall resmda -y
-	rm -rf build/ dist/ .eggs/ resmda.egg-info/ resmda/version.py  # build
+	python -m pip uninstall dageo -y
+	rm -rf build/ dist/ .eggs/ dageo.egg-info/ dageo/version.py  # build
 	rm -rf */__pycache__/ */*/__pycache__/      # python cache
 	rm -rf .coverage htmlcov/ .pytest_cache/    # tests and coverage
-	rm -rf docs/gallery/* docs/gallery/*.zip docs/_build/ docs/api/resmda*  # docs
+	rm -rf docs/gallery/* docs/gallery/*.zip docs/_build/ docs/api/dageo*  # docs
 	rm -rf docs/savefig

README.rst

@@ -1,15 +1,17 @@
-``resmda`` - ES-MDA with a simple 2D reservoir modeller
-=======================================================
+``dageo`` - Data Assimilation in Geosciences
+============================================
 
-A simple 2D reservoir simulator and a straight-forward implementation of the
-basic *Ensemble smoother with multiple data assimilation* (ES-MDA) algorithm as
-presented by Emerick and Reynolds, 2013.
+Data Assimilation in Geosciences is, for now, a simple 2D reservoir simulator
+and a straight-forward implementation of the basic *Ensemble smoother with
+multiple data assimilation* (ESMDA) algorithm as presented by Emerick and
+Reynolds, 2013. However, more DA methods and examples might be added in the
+future.
 
-- **Documentation:** https://tuda-geo.github.io/resmda
-- **Source Code:** https://github.com/tuda-geo/resmda
-- **Bug reports:** https://github.com/tuda-geo/resmda/issues
+- **Documentation:** https://tuda-geo.github.io/dageo
+- **Source Code:** https://github.com/tuda-geo/dageo
+- **Bug reports:** https://github.com/tuda-geo/dageo/issues
 
 
 Available through pip and conda:
-``pip install resmda`` / ``conda install -c conda-forge resmda``.
+``pip install dageo`` / ``conda install -c conda-forge dageo``.
 

resmda/__init__.py → dageo/__init__.py

@@ -1,6 +1,6 @@
 # Copyright 2024 D. Werthmüller, G. Serrao Seabra, F.C. Vossepoel
 #
-# This file is part of resmda.
+# This file is part of dageo.
 #
 # Licensed under the Apache License, Version 2.0 (the "License"); you may not
 # use this file except in compliance with the License.  You may obtain a copy
@@ -14,13 +14,10 @@
 # License for the specific language governing permissions and limitations under
 # the License.
 
-from resmda import utils
-from resmda.utils import localization_matrix, Report
-from resmda.data_assimilation import esmda
-from resmda.reservoir_simulator import Simulator, RandomPermeability
-
-print("Warning: `resmda` will change its name to `dageo`.")
-print("         Install `dageo` to get the newest version.")
+from dageo import utils
+from dageo.utils import localization_matrix, Report
+from dageo.data_assimilation import esmda
+from dageo.reservoir_simulator import Simulator, RandomPermeability
 
 # Initialize a random number generator.
 rng = utils.rng()

resmda/data_assimilation.py → dageo/data_assimilation.py

@@ -1,6 +1,6 @@
 # Copyright 2024 D. Werthmüller, G. Serrao Seabra, F.C. Vossepoel
 #
-# This file is part of resmda.
+# This file is part of dageo.
 #
 # Licensed under the Apache License, Version 2.0 (the "License"); you may not
 # use this file except in compliance with the License.  You may obtain a copy
@@ -16,7 +16,7 @@
 
 import numpy as np
 
-from resmda import utils
+from dageo import utils
 
 __all__ = ['esmda']
 
@@ -28,10 +28,10 @@ def __dir__():
 def esmda(model_prior, forward, data_obs, sigma, alphas=4, data_prior=None,
           localization_matrix=None, callback_post=None, return_post_data=True,
           return_steps=False, random=None):
-    """ES-MDA algorithm ([EmRe13]_) with optional localization.
+    """ESMDA algorithm ([EmRe13]_) with optional localization.
 
     Consult the section :ref:`esmda` in the manual for the theory and more
-    information about ES-MDA.
+    information about ESMDA.
 
     Parameters
     ----------
@@ -48,20 +48,20 @@ def esmda(model_prior, forward, data_obs, sigma, alphas=4, data_prior=None,
     sigma : {float, ndarray}
         Standard deviation(s) of the observation noise.
     alphas : {int, array-like}, default: 4
-        Inflation factors for ES-MDA.
+        Inflation factors for ESMDA.
     data_prior : ndarray, default: None
         Prior data ensemble, of shape ``(ne, nd)``.
     callback_post : function, default: None
-        Function to be executed after each ES-MDA iteration to the posterior
+        Function to be executed after each ESMDA iteration to the posterior
         model, ``callback_post(model_post)``.
     return_post_data : bool, default: True
         If true, returns also ``forward(model_post)``.
     return_steps : bool, default: False
-        If true, returns model and data of all ES-MDA steps. Setting
+        If true, returns model and data of all ESMDA steps. Setting
         ``return_steps`` to True enforces ``return_post_data=True``.
     random : {None, int,  np.random.Generator}, default: None
         Seed or random generator for reproducibility; see
-        :func:`resmda.utils.rng`.
+        :func:`dageo.utils.rng`.
     localization_matrix : {ndarray, None}, default: None
         If provided, apply localization to the Kalman gain matrix, of shape
         ``(model-shape, nd)``.
@@ -97,7 +97,7 @@ def esmda(model_prior, forward, data_obs, sigma, alphas=4, data_prior=None,
 
     # Loop over alphas
     for i, alpha in enumerate(alphas):
-        print(f"ES-MDA step {i+1: 3d}; α={alpha}")
+        print(f"ESMDA step {i+1: 3d}; α={alpha}")
 
         # == Step (a) of Emerick & Reynolds, 2013 ==
         # Run the ensemble from time zero.

resmda/reservoir_simulator.py → dageo/reservoir_simulator.py

@@ -1,6 +1,6 @@
 # Copyright 2024 D. Werthmüller, G. Serrao Seabra, F.C. Vossepoel
 #
-# This file is part of resmda.
+# This file is part of dageo.
 #
 # Licensed under the Apache License, Version 2.0 (the "License"); you may not
 # use this file except in compliance with the License.  You may obtain a copy
@@ -17,7 +17,7 @@
 import numpy as np
 import scipy as sp
 
-from resmda import utils
+from dageo import utils
 
 __all__ = ['Simulator', 'RandomPermeability']
 

resmda/utils.py → dageo/utils.py

@@ -1,6 +1,6 @@
 # Copyright 2024 D. Werthmüller, G. Serrao Seabra, F.C. Vossepoel
 #
-# This file is part of resmda.
+# This file is part of dageo.
 #
 # Licensed under the Apache License, Version 2.0 (the "License"); you may not
 # use this file except in compliance with the License.  You may obtain a copy
@@ -21,7 +21,7 @@
 from scooby import Report as ScoobyReport
 
 try:
-    from resmda.version import version as __version__
+    from dageo.version import version as __version__
 except ImportError:
     __version__ = 'unknown-'+datetime.today().strftime('%Y%m%d')
 
@@ -189,6 +189,6 @@ class Report(ScoobyReport):
     def __init__(self, **kwargs):
         """Initiate a scooby.Report instance."""
         kwargs = {'ncol': 3, **kwargs}
-        kwargs['core'] = ['resmda', 'numpy', 'scipy']
+        kwargs['core'] = ['dageo', 'numpy', 'scipy']
         kwargs['optional'] = ['matplotlib', 'IPython']
         super().__init__(**kwargs)

docs/Makefile

@@ -1,7 +1,7 @@
 # Command line options.
 SPHINXOPTS    =
 SPHINXBUILD   = sphinx-build
-SPHINXPROJ    = resmda
+SPHINXPROJ    = dageo
 SOURCEDIR     = .
 BUILDDIR      = _build
 

docs/api/data_assimilation.rst

@@ -1,6 +1,6 @@
 Data Assimilation
 -----------------
 
-.. automodapi:: resmda.data_assimilation
+.. automodapi:: dageo.data_assimilation
    :no-inheritance-diagram:
    :no-heading:

docs/api/index.rst

@@ -9,7 +9,7 @@ API reference
 
 ----
 
-.. module:: resmda
+.. module:: dageo
 
 
 .. toctree::

docs/api/reservoir_simulator.rst

@@ -1,6 +1,6 @@
 Reservoir Simulator
 -------------------
 
-.. automodapi:: resmda.reservoir_simulator
+.. automodapi:: dageo.reservoir_simulator
    :no-inheritance-diagram:
    :no-heading:

docs/api/utils.rst

@@ -1,6 +1,6 @@
 Utilities
 ---------
 
-.. automodapi:: resmda.utils
+.. automodapi:: dageo.utils
    :no-inheritance-diagram:
    :no-heading:

docs/conf.py

@@ -1,6 +1,6 @@
 import time
 import warnings
-from resmda import __version__
+from dageo import __version__
 
 # ==== 1. Extensions  ====
 
@@ -64,7 +64,7 @@
 }
 
 # ==== 2. General Settings ====
-description = "ES-MDA with a simple 2D reservoir modeller"
+description = "Data Assimilation in Geosciences"
 
 # The templates path.
 # templates_path = ["_templates"]
@@ -76,7 +76,7 @@
 master_doc = "index"
 
 # General information about the project.
-project = "resmda"
+project = "dageo"
 author = "D. Werthmüller, G. Serrao Seabra, F.C. Vossepoel"
 copyright = f"2024-{time.strftime('%Y')}, {author}"
 
@@ -99,23 +99,23 @@
 
 html_theme_options = {
     "logo": {
-        "text": "resmda",
+        "text": "dageo",
     },
     "navigation_with_keys": True,
-    "github_url": "https://github.com/tuda-geo/resmda",
+    "github_url": "https://github.com/tuda-geo/dageo",
     # "use_edit_page_button": True,
 }
 
 html_context = {
     "github_user": "tuda-geo",
-    "github_repo": "resmda",
+    "github_repo": "dageo",
     "github_version": "main",
     "doc_path": "docs",
 }
 
 html_use_modindex = True
 html_file_suffix = ".html"
-htmlhelp_basename = "resmda"
+htmlhelp_basename = "dageo"
 html_css_files = [
     "style.css",
     "https://cdnjs.cloudflare.com/ajax/libs/font-awesome/4.7.0/" +

docs/index.rst

@@ -1,12 +1,12 @@
-.. _resmda-manual:
+.. _dageo-manual:
 
-####################
-resmda Documentation
-####################
+###################
+dageo Documentation
+###################
 
 :Release: |version|
 :Date: |today|
-:Source: `github.com/tuda-geo/resmda <https://github.com/tuda-geo/resmda>`_
+:Source: `github.com/tuda-geo/dageo <https://github.com/tuda-geo/dageo>`_
 
 ----
 
@@ -47,13 +47,13 @@ resmda Documentation
         Gallery
         ^^^^^^^
 
-        The gallery contains examples on the usage of resmda, and is generally
+        The gallery contains examples on the usage of dageo, and is generally
         the best way to get started. Download them and modify them to your
         needs!
 
         +++
 
-        .. button-ref:: resmda_gallery
+        .. button-ref:: dageo_gallery
             :expand:
             :color: info
             :click-parent:
@@ -67,7 +67,7 @@ resmda Documentation
         API reference
         ^^^^^^^^^^^^^
 
-        The API reference of resmda includes almost every function and class.
+        The API reference of dageo includes almost every function and class.
         Some of the underlying theory is also described in the docstrings.
 
         +++