From 7eff8a9c11211380a95c1da3ae2b3e988e4bdd34 Mon Sep 17 00:00:00 2001 From: Jeff Klenzing Date: Wed, 24 Apr 2019 21:33:18 -0400 Subject: [PATCH 01/20] update code --- docs/installation.rst | 1 - 1 file changed, 1 deletion(-) diff --git a/docs/installation.rst b/docs/installation.rst index d7c1dc7a..0b7ef6bf 100644 --- a/docs/installation.rst +++ b/docs/installation.rst @@ -3,7 +3,6 @@ Installation First, checkout the repository:: -.. code:: python git clone git@gitlab.com:jklenzing/sami2py.git Change directories into the repository folder and run the setup.py file. For From 95c28aff6821779c941f745c3598d1464723cc5e Mon Sep 17 00:00:00 2001 From: Jeff Klenzing Date: Wed, 24 Apr 2019 21:49:38 -0400 Subject: [PATCH 02/20] Added badge --- README.md | 1 + 1 file changed, 1 insertion(+) diff --git a/README.md b/README.md index c28f41c0..e65dba36 100644 --- a/README.md +++ b/README.md @@ -1,6 +1,7 @@ # sami2py: sami2py is another model of the ionosphere python style [![Build Status](https://travis-ci.com/jklenzing/sami2py.svg?branch=master)](https://travis-ci.org/jklenzing/sami2py) +[![Documentation Status](https://readthedocs.org/projects/sami2py/badge/?version=latest)](http://pysat.readthedocs.io/en/latest/?badge=latest) # Overview From 79ba98cffb282a5f865804920bfb89e37187d959 Mon Sep 17 00:00:00 2001 From: Jeff Klenzing Date: Wed, 24 Apr 2019 21:51:03 -0400 Subject: [PATCH 03/20] show as code --- docs/installation.rst | 2 +- docs/sample_workflow.rst | 9 +++++---- 2 files changed, 6 insertions(+), 5 deletions(-) diff --git a/docs/installation.rst b/docs/installation.rst index 0b7ef6bf..d4cccaec 100644 --- a/docs/installation.rst +++ b/docs/installation.rst @@ -1,7 +1,7 @@ Installation ============ -First, checkout the repository:: +First, checkout the repository: git clone git@gitlab.com:jklenzing/sami2py.git diff --git a/docs/sample_workflow.rst b/docs/sample_workflow.rst index 0cb5887d..a3ddbabf 100644 --- a/docs/sample_workflow.rst +++ b/docs/sample_workflow.rst @@ -3,14 +3,15 @@ Sample Workflow In iPython, run: -``` +.. code:: python import sami2py sami2py.run_model(year=2012, day=210, lon=0, tag='test') -``` + Note that the sami2 model runs for 24 hours to clear transients, then begins to output data. Now load the resultant data: -``` +.. code:: python ModelRun = sami2py.model(tag='test', lon=0, year=2012, day=210) -``` + +Full description coming soon From 46d6760ff5340def8ab1359575a1405df2a4f2e3 Mon Sep 17 00:00:00 2001 From: Jeff Klenzing Date: Wed, 24 Apr 2019 21:54:18 -0400 Subject: [PATCH 04/20] add requirements --- docs/requirements.txt | 2 ++ 1 file changed, 2 insertions(+) create mode 100644 docs/requirements.txt diff --git a/docs/requirements.txt b/docs/requirements.txt new file mode 100644 index 00000000..1ff8ec63 --- /dev/null +++ b/docs/requirements.txt @@ -0,0 +1,2 @@ +numpydoc +ipython From 88a6c2801555fb6e588d7bf7690afe2bad20b4fd Mon Sep 17 00:00:00 2001 From: Jeff Klenzing Date: Wed, 24 Apr 2019 21:58:05 -0400 Subject: [PATCH 05/20] add packages --- docs/conf.py | 6 +++++- 1 file changed, 5 insertions(+), 1 deletion(-) diff --git a/docs/conf.py b/docs/conf.py index fc1c1f60..63d210ec 100644 --- a/docs/conf.py +++ b/docs/conf.py @@ -38,7 +38,11 @@ # Add any Sphinx extension module names here, as strings. They can be # extensions coming with Sphinx (named 'sphinx.ext.*') or your custom # ones. -extensions = ['recommonmark'] +extensions = [ + 'recommonmark' + 'numpydoc', + 'IPython.sphinxext.ipython_console_highlighting' +] # Add any paths that contain templates here, relative to this directory. templates_path = ['_templates'] From 71f3932409a2446a112da2c1560941d4d66e630e Mon Sep 17 00:00:00 2001 From: Jeff Klenzing Date: Wed, 24 Apr 2019 22:01:27 -0400 Subject: [PATCH 06/20] typo --- docs/conf.py | 2 +- 1 file changed, 1 insertion(+), 1 deletion(-) diff --git a/docs/conf.py b/docs/conf.py index 63d210ec..7a72c8b1 100644 --- a/docs/conf.py +++ b/docs/conf.py @@ -39,7 +39,7 @@ # extensions coming with Sphinx (named 'sphinx.ext.*') or your custom # ones. extensions = [ - 'recommonmark' + 'recommonmark', 'numpydoc', 'IPython.sphinxext.ipython_console_highlighting' ] From 6598f2ae132c594a18677792d8a89b1e7a9ee127 Mon Sep 17 00:00:00 2001 From: Jeff Klenzing Date: Wed, 24 Apr 2019 22:14:36 -0400 Subject: [PATCH 07/20] updates to refs --- README.md | 2 +- 1 file changed, 1 insertion(+), 1 deletion(-) diff --git a/README.md b/README.md index e65dba36..9d01af2c 100644 --- a/README.md +++ b/README.md @@ -65,4 +65,4 @@ work uses the SAMI2 ionosphere model written and developed by the Naval Research # References - Huba, J.D., G. Joyce, and J.A. Fedder, Sami2 is Another Model of the Ionosphere (SAMI2): A new low‐latitude ionosphere model, *J. Geophys. Res.*, 105, Pages 23035-23053, https://doi.org/10.1029/2000JA000035, 2000. - Emmert, J.T., J.L. Lean, and J.M. Picone, Record‐low thermospheric density during the 2008 solar minimum, *Geophys. Res. Lett.*, 37, https://doi.org/10.1029/2010GL043671, 2010. -- Klenzing, J., Burrell, A. G., Heelis, R. A., Huba, J. D., Pfaff, R., and Simões, F.: Exploring the role of ionospheric drivers during the extreme solar minimum of 2008, *Ann. Geophys.*, 31, 2147-2156, https://doi.org/10.5194/angeo-31-2147-2013, 2013. +- Klenzing, J., A. G. Burrell, R. A. Heelis, J. D. Huba, R. Pfaff, and F. Simões, Exploring the role of ionospheric drivers during the extreme solar minimum of 2008, *Ann. Geophys.*, 31, 2147-2156, https://doi.org/10.5194/angeo-31-2147-2013, 2013. From 5b4b52af694a592dc467b02d1ee434278eb37550 Mon Sep 17 00:00:00 2001 From: Jeff Klenzing Date: Wed, 24 Apr 2019 22:19:33 -0400 Subject: [PATCH 08/20] updates --- docs/conf.py | 6 ++++-- 1 file changed, 4 insertions(+), 2 deletions(-) diff --git a/docs/conf.py b/docs/conf.py index 7a72c8b1..976ac56a 100644 --- a/docs/conf.py +++ b/docs/conf.py @@ -21,10 +21,10 @@ project = 'sami2py' copyright = '2019, Jeff Klenzing' -author = 'Jeff Klenzing' +author = 'Jeff Klenzing \\and Jonathon Smith' # The short X.Y version -version = '' +version = '0.1a2' # The full version, including alpha/beta/rc tags release = '' @@ -44,6 +44,8 @@ 'IPython.sphinxext.ipython_console_highlighting' ] +numpydoc_show_class_members = False + # Add any paths that contain templates here, relative to this directory. templates_path = ['_templates'] From 1f965c7ac300607d50f8331aad847a42c1128758 Mon Sep 17 00:00:00 2001 From: Jeff Klenzing Date: Wed, 24 Apr 2019 22:21:37 -0400 Subject: [PATCH 09/20] add extensions --- docs/conf.py | 6 ++++++ 1 file changed, 6 insertions(+) diff --git a/docs/conf.py b/docs/conf.py index 976ac56a..ed11d022 100644 --- a/docs/conf.py +++ b/docs/conf.py @@ -39,6 +39,12 @@ # extensions coming with Sphinx (named 'sphinx.ext.*') or your custom # ones. extensions = [ + 'sphinx.ext.autodoc', + 'sphinx.ext.doctest', + 'sphinx.ext.todo', + 'sphinx.ext.imgmath', + 'sphinx.ext.autosummary', + 'sphinx.ext.napoleon', 'recommonmark', 'numpydoc', 'IPython.sphinxext.ipython_console_highlighting' From c84772167d7ad8c08a01a40b9f9a947a2b1146a1 Mon Sep 17 00:00:00 2001 From: Jeff Klenzing Date: Wed, 24 Apr 2019 22:23:11 -0400 Subject: [PATCH 10/20] spacing --- docs/sample_workflow.rst | 2 ++ 1 file changed, 2 insertions(+) diff --git a/docs/sample_workflow.rst b/docs/sample_workflow.rst index a3ddbabf..9095010b 100644 --- a/docs/sample_workflow.rst +++ b/docs/sample_workflow.rst @@ -4,6 +4,7 @@ Sample Workflow In iPython, run: .. code:: python + import sami2py sami2py.run_model(year=2012, day=210, lon=0, tag='test') @@ -12,6 +13,7 @@ Note that the sami2 model runs for 24 hours to clear transients, then begins to Now load the resultant data: .. code:: python + ModelRun = sami2py.model(tag='test', lon=0, year=2012, day=210) Full description coming soon From 50c2c566315be8b35eec96fa73445d606860fa07 Mon Sep 17 00:00:00 2001 From: Jeff Klenzing Date: Wed, 24 Apr 2019 22:28:34 -0400 Subject: [PATCH 11/20] updates to intro --- docs/introduction.rst | 6 +++--- 1 file changed, 3 insertions(+), 3 deletions(-) diff --git a/docs/introduction.rst b/docs/introduction.rst index 241d6c6e..8790c322 100644 --- a/docs/introduction.rst +++ b/docs/introduction.rst @@ -12,7 +12,7 @@ The implementation used here includes several added options to the original rele The open-source fortran version of SAMI2 is found at https://www.nrl.navy.mil/ppd/branches/6790/sami2 How to Cite - =========== + ----------- When referring to this software package, please cite the original paper by Huba et al [2000] https://doi.org/10.1029/2000JA000035 as well as the package by Klenzing et al [2018]. ***add doi here***. @@ -20,8 +20,8 @@ The open-source fortran version of SAMI2 is found at https://www.nrl.navy.mil/pp work uses the SAMI2 ionosphere model written and developed by the Naval Research Laboratory." References - ========== + ---------- - Huba, J.D., G. Joyce, and J.A. Fedder, Sami2 is Another Model of the Ionosphere (SAMI2): A new low‐latitude ionosphere model, *J. Geophys. Res.*, 105, Pages 23035-23053, https://doi.org/10.1029/2000JA000035, 2000. - Emmert, J.T., J.L. Lean, and J.M. Picone, Record‐low thermospheric density during the 2008 solar minimum, *Geophys. Res. Lett.*, 37, https://doi.org/10.1029/2010GL043671, 2010. - - Klenzing, J., Burrell, A. G., Heelis, R. A., Huba, J. D., Pfaff, R., and Simões, F.: Exploring the role of ionospheric drivers during the extreme solar minimum of 2008, *Ann. Geophys.*, 31, 2147-2156, https://doi.org/10.5194/angeo-31-2147-2013, 2013. + - Klenzing, J., A. G. Burrell, R. A. Heelis, J. D. Huba, R. Pfaff, and F. Simões, Exploring the role of ionospheric drivers during the extreme solar minimum of 2008, *Ann. Geophys.*, 31, 2147-2156, https://doi.org/10.5194/angeo-31-2147-2013, 2013. From bb58f5a799ee29ee6c5e13475b11ae4ba8ee54bb Mon Sep 17 00:00:00 2001 From: Jeff Klenzing Date: Wed, 24 Apr 2019 22:30:14 -0400 Subject: [PATCH 12/20] html --- docs/introduction.rst | 4 ++++ 1 file changed, 4 insertions(+) diff --git a/docs/introduction.rst b/docs/introduction.rst index 8790c322..80282469 100644 --- a/docs/introduction.rst +++ b/docs/introduction.rst @@ -1,4 +1,8 @@ +.. |br| raw:: html + +
+ Introduction ============ From a350f791fe8018db0ff68d3c86712477b4beb7b4 Mon Sep 17 00:00:00 2001 From: Jeff Klenzing Date: Thu, 25 Apr 2019 08:03:56 -0400 Subject: [PATCH 13/20] spacing --- docs/introduction.rst | 17 +++++++++-------- 1 file changed, 9 insertions(+), 8 deletions(-) diff --git a/docs/introduction.rst b/docs/introduction.rst index 80282469..119e4499 100644 --- a/docs/introduction.rst +++ b/docs/introduction.rst @@ -2,7 +2,7 @@ .. |br| raw:: html
- + Introduction ============ @@ -15,16 +15,17 @@ The implementation used here includes several added options to the original rele The open-source fortran version of SAMI2 is found at https://www.nrl.navy.mil/ppd/branches/6790/sami2 - How to Cite - ----------- - When referring to this software package, please cite the original paper by Huba et al [2000] https://doi.org/10.1029/2000JA000035 as well as the package by Klenzing et al [2018]. ***add doi here***. +How to Cite +----------- + +When referring to this software package, please cite the original paper by Huba et al [2000] https://doi.org/10.1029/2000JA000035 as well as the package by Klenzing et al [2018]. ***add doi here***. + +Additionally, please include the following text in the acknowledgements: "This work uses the SAMI2 ionosphere model written and developed by the Naval Research Laboratory." - Additionally, please include the following text in the acknowledgements: "This - work uses the SAMI2 ionosphere model written and developed by the Naval Research Laboratory." - References - ---------- +References +---------- - Huba, J.D., G. Joyce, and J.A. Fedder, Sami2 is Another Model of the Ionosphere (SAMI2): A new low‐latitude ionosphere model, *J. Geophys. Res.*, 105, Pages 23035-23053, https://doi.org/10.1029/2000JA000035, 2000. - Emmert, J.T., J.L. Lean, and J.M. Picone, Record‐low thermospheric density during the 2008 solar minimum, *Geophys. Res. Lett.*, 37, https://doi.org/10.1029/2010GL043671, 2010. From bffca04e7e016ee16925e5e746d237579b990e8d Mon Sep 17 00:00:00 2001 From: Jeff Klenzing Date: Thu, 25 Apr 2019 08:08:33 -0400 Subject: [PATCH 14/20] test --- docs/introduction.rst | 2 +- 1 file changed, 1 insertion(+), 1 deletion(-) diff --git a/docs/introduction.rst b/docs/introduction.rst index 119e4499..aaa68579 100644 --- a/docs/introduction.rst +++ b/docs/introduction.rst @@ -6,7 +6,7 @@ Introduction ============ -Sami2py is a python module that runs the SAMI2 model, as well as archives, loads and plots the resulting modeled values. SAMI2 is a model developed by the Naval Research Laboratory to simulate the motions of plasma in a 2D ionospheric environment along a dipole magnetic field [Huba et al, 2000]. SAMI2 solves for the chemical and dynamical evolution of seven ion species in this environment (H+, He+, N+, O+, N2+, NO+, and O2+). +Sami2py is a python module that runs the SAMI2 model, as well as archives, loads and plots the resulting modeled values. SAMI2 is a model developed by the Naval Research Laboratory to simulate the motions of plasma in a 2D ionospheric environment along a dipole magnetic field [Huba et al, 2000]. SAMI2 solves for the chemical and dynamical evolution of seven ion species in this environment (H+, He+, N+, O+, N2+, NO+, and O\ :sub:`2`\+). The implementation used here includes several added options to the original release of SAMI2. A full list is included in ***add link to changes page***, but several of these include: - The ability to scale the neutral atmosphere in which the ions form through direct modification of the exospheric neutral temperature for extreme solar minimum conditions, as discussed by Emmert et al [2010]. From dc86967589dee0b33f838a0d5d7c55aad9f5d5c1 Mon Sep 17 00:00:00 2001 From: Jeff Klenzing Date: Thu, 25 Apr 2019 08:10:25 -0400 Subject: [PATCH 15/20] test --- docs/introduction.rst | 2 +- 1 file changed, 1 insertion(+), 1 deletion(-) diff --git a/docs/introduction.rst b/docs/introduction.rst index aaa68579..4a2c0f6a 100644 --- a/docs/introduction.rst +++ b/docs/introduction.rst @@ -6,7 +6,7 @@ Introduction ============ -Sami2py is a python module that runs the SAMI2 model, as well as archives, loads and plots the resulting modeled values. SAMI2 is a model developed by the Naval Research Laboratory to simulate the motions of plasma in a 2D ionospheric environment along a dipole magnetic field [Huba et al, 2000]. SAMI2 solves for the chemical and dynamical evolution of seven ion species in this environment (H+, He+, N+, O+, N2+, NO+, and O\ :sub:`2`\+). +Sami2py is a python module that runs the SAMI2 model, as well as archives, loads and plots the resulting modeled values. SAMI2 is a model developed by the Naval Research Laboratory to simulate the motions of plasma in a 2D ionospheric environment along a dipole magnetic field [Huba et al, 2000]. SAMI2 solves for the chemical and dynamical evolution of seven ion species in this environment (H+, He+, N+, O+, N2+, NO+, and O\ :sub:`2`\\ :sup:`+`\). The implementation used here includes several added options to the original release of SAMI2. A full list is included in ***add link to changes page***, but several of these include: - The ability to scale the neutral atmosphere in which the ions form through direct modification of the exospheric neutral temperature for extreme solar minimum conditions, as discussed by Emmert et al [2010]. From 1b6f5575878d2858afcb159897d6f4ec1c0a6a89 Mon Sep 17 00:00:00 2001 From: Jeff Klenzing Date: Thu, 25 Apr 2019 08:12:34 -0400 Subject: [PATCH 16/20] format sub and superscript --- docs/introduction.rst | 2 +- 1 file changed, 1 insertion(+), 1 deletion(-) diff --git a/docs/introduction.rst b/docs/introduction.rst index 4a2c0f6a..c68849cf 100644 --- a/docs/introduction.rst +++ b/docs/introduction.rst @@ -6,7 +6,7 @@ Introduction ============ -Sami2py is a python module that runs the SAMI2 model, as well as archives, loads and plots the resulting modeled values. SAMI2 is a model developed by the Naval Research Laboratory to simulate the motions of plasma in a 2D ionospheric environment along a dipole magnetic field [Huba et al, 2000]. SAMI2 solves for the chemical and dynamical evolution of seven ion species in this environment (H+, He+, N+, O+, N2+, NO+, and O\ :sub:`2`\\ :sup:`+`\). +Sami2py is a python module that runs the SAMI2 model, as well as archives, loads and plots the resulting modeled values. SAMI2 is a model developed by the Naval Research Laboratory to simulate the motions of plasma in a 2D ionospheric environment along a dipole magnetic field [Huba et al, 2000]. SAMI2 solves for the chemical and dynamical evolution of seven ion species in this environment (H\ :sup:`+`\, He\ :sup:`+`\, N\ :sup:`+`\, O\ :sup:`+`\, N\ :sub:`2` :sup:`+`\, NO\ :sup:`+`\, and O\ :sub:`2` :sup:`+`\). The implementation used here includes several added options to the original release of SAMI2. A full list is included in ***add link to changes page***, but several of these include: - The ability to scale the neutral atmosphere in which the ions form through direct modification of the exospheric neutral temperature for extreme solar minimum conditions, as discussed by Emmert et al [2010]. From ad111e14c858b2b2e8e4406e9cb21381d19124ad Mon Sep 17 00:00:00 2001 From: Jeff Klenzing Date: Thu, 25 Apr 2019 08:16:29 -0400 Subject: [PATCH 17/20] format terminal commands --- docs/installation.rst | 6 ++++++ 1 file changed, 6 insertions(+) diff --git a/docs/installation.rst b/docs/installation.rst index d4cccaec..f6736bf9 100644 --- a/docs/installation.rst +++ b/docs/installation.rst @@ -3,16 +3,22 @@ Installation First, checkout the repository: +:: + git clone git@gitlab.com:jklenzing/sami2py.git Change directories into the repository folder and run the setup.py file. For a local install use the "--user" flag after "install". +:: + cd sami2py/ python setup.py install Additionally, you must make and install the fortran executables. +:: + make -C sami2py/fortran compile Now you can run the sami2 executable (sami2py.x) from anywhere. From 05dfd187d0aa25490310a16f38cf7e7103f32583 Mon Sep 17 00:00:00 2001 From: Jeff Klenzing Date: Thu, 25 Apr 2019 08:19:01 -0400 Subject: [PATCH 18/20] ipython formatting --- docs/sample_workflow.rst | 4 ++-- 1 file changed, 2 insertions(+), 2 deletions(-) diff --git a/docs/sample_workflow.rst b/docs/sample_workflow.rst index 9095010b..f284c53a 100644 --- a/docs/sample_workflow.rst +++ b/docs/sample_workflow.rst @@ -3,7 +3,7 @@ Sample Workflow In iPython, run: -.. code:: python +.. ipython:: import sami2py sami2py.run_model(year=2012, day=210, lon=0, tag='test') @@ -12,7 +12,7 @@ Note that the sami2 model runs for 24 hours to clear transients, then begins to Now load the resultant data: -.. code:: python +.. ipython:: ModelRun = sami2py.model(tag='test', lon=0, year=2012, day=210) From b721c718f9465343cb21e1da21e8b3570739b334 Mon Sep 17 00:00:00 2001 From: Jeff Klenzing Date: Thu, 25 Apr 2019 08:21:27 -0400 Subject: [PATCH 19/20] revert format --- docs/sample_workflow.rst | 4 ++-- 1 file changed, 2 insertions(+), 2 deletions(-) diff --git a/docs/sample_workflow.rst b/docs/sample_workflow.rst index f284c53a..9095010b 100644 --- a/docs/sample_workflow.rst +++ b/docs/sample_workflow.rst @@ -3,7 +3,7 @@ Sample Workflow In iPython, run: -.. ipython:: +.. code:: python import sami2py sami2py.run_model(year=2012, day=210, lon=0, tag='test') @@ -12,7 +12,7 @@ Note that the sami2 model runs for 24 hours to clear transients, then begins to Now load the resultant data: -.. ipython:: +.. code:: python ModelRun = sami2py.model(tag='test', lon=0, year=2012, day=210) From ab9f3baa1b808656b0120b9d778821c5c34f668b Mon Sep 17 00:00:00 2001 From: Jeff Klenzing Date: Thu, 25 Apr 2019 15:03:23 -0400 Subject: [PATCH 20/20] Update README.md --- README.md | 2 +- 1 file changed, 1 insertion(+), 1 deletion(-) diff --git a/README.md b/README.md index 9d01af2c..ef8ec2ff 100644 --- a/README.md +++ b/README.md @@ -1,7 +1,7 @@ # sami2py: sami2py is another model of the ionosphere python style [![Build Status](https://travis-ci.com/jklenzing/sami2py.svg?branch=master)](https://travis-ci.org/jklenzing/sami2py) -[![Documentation Status](https://readthedocs.org/projects/sami2py/badge/?version=latest)](http://pysat.readthedocs.io/en/latest/?badge=latest) +[![Documentation Status](https://readthedocs.org/projects/sami2py/badge/?version=latest)](http://sami2py.readthedocs.io/en/latest/?badge=latest) # Overview