From a0a222dd2e222daa5a0f6d44fcc8f7f238d3c6f0 Mon Sep 17 00:00:00 2001
From: Ben Preston <144227999+ben-l-p@users.noreply.github.com>
Date: Wed, 4 Oct 2023 16:06:54 +0100
Subject: [PATCH 01/15] Add files via upload

---
 utils/environment_macos_arm64.yml | 96 +++++++++++++++++++++++++++++++
 1 file changed, 96 insertions(+)
 create mode 100644 utils/environment_macos_arm64.yml

diff --git a/utils/environment_macos_arm64.yml b/utils/environment_macos_arm64.yml
new file mode 100644
index 000000000..ad9f12981
--- /dev/null
+++ b/utils/environment_macos_arm64.yml
@@ -0,0 +1,96 @@
+name: sharpy_env
+channels:
+  - conda-forge
+  - defaults
+dependencies:
+  - alabaster
+  - apptools
+  - blas
+  - bzip2
+  - ca-certificates
+  - certifi
+  - cmake
+  - colorama
+  - configobj
+  - control
+  - coverage
+  - curl
+  - cycler
+  - dbus
+  - dill
+  - eigen
+  - envisage
+  - expat
+  - freetype
+  - future
+  - gettext
+  - glib
+  - h5py
+  - hdf4
+  - hdf5
+  - icu
+  - jpeg
+  - jsoncpp
+  - kiwisolver
+  - krb5
+  - libcurl
+  - libcxx
+  - libedit
+  - libffi
+  - libgfortran
+  - libiconv
+  - libnetcdf
+  - libogg
+  - libopenblas
+  - libpng
+  - libssh2
+  - libtheora
+  - libtiff
+  - libvorbis
+  - libxml2
+  - libxslt
+  - lxml
+  - lz4-c
+  - matplotlib
+  - matplotlib-base
+  - mayavi
+  - ncurses
+  - numpy
+  - numpy-base
+  - openblas
+  - openssl
+  - pandas
+  - pcre
+  - pip
+  - pyface
+  - pygments
+  - pyparsing
+  - pyqt
+  - python
+  - python-dateutil
+  - python_abi
+  - pytz
+  - pyyaml
+  - qt
+  - readline
+  - rhash
+  - scipy
+  - setuptools
+  - sip
+  - six
+  - slycot
+  - sqlite
+  - tbb
+  - tk
+  - tornado
+  - traits
+  - traitsui
+  - vtk
+  - wheel
+  - xlrd
+  - xz
+  - yaml
+  - zlib
+  - zstd
+  - openpyxl
+

From a73686112b58b6351ba84abdd7584ff7ad36983f Mon Sep 17 00:00:00 2001
From: Ben Preston <144227999+ben-l-p@users.noreply.github.com>
Date: Mon, 9 Oct 2023 10:08:20 +0100
Subject: [PATCH 02/15] Update environment_macos_arm64.yml

Replaced environment file to use the new environment. Only change is the less strict make version requirement.
---
 utils/environment_macos_arm64.yml | 114 ++++++------------------------
 1 file changed, 22 insertions(+), 92 deletions(-)

diff --git a/utils/environment_macos_arm64.yml b/utils/environment_macos_arm64.yml
index ad9f12981..f2642e411 100644
--- a/utils/environment_macos_arm64.yml
+++ b/utils/environment_macos_arm64.yml
@@ -1,96 +1,26 @@
-name: sharpy_env
+name: sharpy
 channels:
   - conda-forge
   - defaults
 dependencies:
-  - alabaster
-  - apptools
-  - blas
-  - bzip2
-  - ca-certificates
-  - certifi
-  - cmake
-  - colorama
-  - configobj
-  - control
-  - coverage
-  - curl
-  - cycler
-  - dbus
-  - dill
-  - eigen
-  - envisage
-  - expat
-  - freetype
-  - future
-  - gettext
-  - glib
-  - h5py
-  - hdf4
-  - hdf5
-  - icu
-  - jpeg
-  - jsoncpp
-  - kiwisolver
-  - krb5
-  - libcurl
-  - libcxx
-  - libedit
-  - libffi
-  - libgfortran
-  - libiconv
-  - libnetcdf
-  - libogg
-  - libopenblas
-  - libpng
-  - libssh2
-  - libtheora
-  - libtiff
-  - libvorbis
-  - libxml2
-  - libxslt
-  - lxml
-  - lz4-c
-  - matplotlib
-  - matplotlib-base
-  - mayavi
-  - ncurses
-  - numpy
-  - numpy-base
-  - openblas
-  - openssl
-  - pandas
-  - pcre
-  - pip
-  - pyface
-  - pygments
-  - pyparsing
-  - pyqt
-  - python
-  - python-dateutil
-  - python_abi
-  - pytz
-  - pyyaml
-  - qt
-  - readline
-  - rhash
-  - scipy
-  - setuptools
-  - sip
-  - six
-  - slycot
-  - sqlite
-  - tbb
-  - tk
-  - tornado
-  - traits
-  - traitsui
-  - vtk
-  - wheel
-  - xlrd
-  - xz
-  - yaml
-  - zlib
-  - zstd
-  - openpyxl
-
+  - asn1crypto>=1.2.0      
+  - colorama>=0.4.1        
+  - control>=0.8.4         
+  - dill>=0.3.1.1          
+  - h5py>=2.9.0            
+  - jupyterlab>=1.2.3      
+  - lxml>=4.4.1            
+  - mayavi>=4.7.1          
+  - nbsphinx>=0.4.3        
+  - pandas>=0.25.3         
+  - pyOpenSSL>=19.0.0      
+  - PySocks>=1.7.1         
+  - PyYAML>=5.1.2          
+  - recommonmark>=0.6.0    
+  - slycot>=0.4.0
+  - sphinx_rtd_theme>=0.4.3
+  - wheel>=0.33.6          
+  - xlrd>=1.2.0            
+  - python=3.10
+  - openpyxl>=3.0.10
+  - cmake>=3.14.0

From aa871954b93d4dd67a056bd4f574850fc1b6986c Mon Sep 17 00:00:00 2001
From: Ben Preston <144227999+ben-l-p@users.noreply.github.com>
Date: Mon, 9 Oct 2023 10:39:31 +0100
Subject: [PATCH 03/15] Update installation instructions

---
 docs/source/content/installation.md | 9 +++++----
 1 file changed, 5 insertions(+), 4 deletions(-)

diff --git a/docs/source/content/installation.md b/docs/source/content/installation.md
index e9cb91a2a..dbd104c71 100644
--- a/docs/source/content/installation.md
+++ b/docs/source/content/installation.md
@@ -1,5 +1,5 @@
 # SHARPy v2.0 Installation Guide
-__Last revision 27 June 2023__
+__Last revision 9 October 2023__
 
 The following step by step tutorial will guide you through the installation process of SHARPy. This is the updated process valid from v2.0.
 
@@ -11,7 +11,8 @@ SHARPy is being developed and tested on the following operating systems:
 * CentOS 7 and CentOS 8
 * Ubuntu 18.04 LTS
 * Debian 10
-* MacOS Mojave and Catalina
+* MacOS Mojave and Catalina (Intel)
+* MacOS Sonoma (Apple Silicon M2)
 
 Windows users can also run it by first installing the Windows Subsystem for Linux (https://learn.microsoft.com/en-us/windows/wsl/install) and a XServer such as GWSL, which can be installed through the Microsoft Store. SHARPy is also available to the vast majority of operating systems that are supported by Docker
 
@@ -72,7 +73,7 @@ or running any SHARPy cases.
     ```
    
 4. Create the conda environment that SHARPy will use. Change `environment_new.yml` to read `environment_macos.yml`
-   if you are installing SHARPy on Mac OS X.
+   if you are installing SHARPy on MacOS (Intel), or `environment_macos_arm64.yml` if installing on macOS (Apple Silicon).
     ```bash
     cd sharpy/utils
     conda env create -f environment_new.yml
@@ -156,7 +157,7 @@ to your taste.
     This command will check out the `develop` branch and set it to track the remote origin. It will also set the submodules (xbeam and UVLM) to the right commit.
 
 2. Create the conda environment that SHARPy will use. Change `environment_new.yml` to read `environment_macos.yml`
-   if you are installing SHARPy on Mac OS X.
+   if you are installing SHARPy on MacOS (Intel), or `environment_macos_arm64.yml` if installing on macOS (Apple Silicon).
     ```bash
     cd sharpy/utils
     conda env create -f environment_new.yml

From 1211514bd2393d3264cbd2b01c82e3cb108c74bf Mon Sep 17 00:00:00 2001
From: Ben Preston <144227999+ben-l-p@users.noreply.github.com>
Date: Wed, 18 Oct 2023 09:13:10 +0100
Subject: [PATCH 04/15] Delete utils/environment_macos.yml

Old MacOS environment is to be replaced with the new environment
---
 utils/environment_macos.yml | 103 ------------------------------------
 1 file changed, 103 deletions(-)
 delete mode 100644 utils/environment_macos.yml

diff --git a/utils/environment_macos.yml b/utils/environment_macos.yml
deleted file mode 100644
index 740bc301b..000000000
--- a/utils/environment_macos.yml
+++ /dev/null
@@ -1,103 +0,0 @@
-name: sharpy_env
-channels:
-  - conda-forge
-  - defaults
-dependencies:
-  - _libgcc_mutex=0.1=main
-  - alabaster=0.7.12=py37_0
-  - apptools=4.4.0=py37_1
-  - blas=1.0=mkl
-  - bzip2=1.0.8=h01d97ff_1
-  - ca-certificates=2020.10.14=0
-  - certifi=2020.6.20=py37_0
-  - cmake=3.14.0=haff7e42_0
-  - colorama=0.4.1=py37_0
-  - configobj=5.0.6=py37_1
-  - control=0.8.4=py37hf985489_0
-  - coverage=4.5.4=py37h1de35cc_0
-  - curl=7.67.0=ha441bb4_0
-  - cycler=0.10.0=py37_0
-  - dbus=1.13.12=h90a0687_0
-  - dill=0.3.1.1=py37_0
-  - eigen=3.3.7=h04f5b5a_1000
-  - envisage=4.8.0=py_0
-  - expat=2.2.6=h0a44026_0
-  - freetype=2.9.1=hb4e5f40_0
-  - future=0.18.2=py37_0
-  - gettext=0.19.8.1=h15daf44_3
-  - glib=2.63.1=hd977a24_0
-  - h5py=2.9.0=py37h3134771_0
-  - hdf4=4.2.13=h39711bb_2
-  - hdf5=1.10.4=hfa1e0ec_0
-  - icu=58.2=h4b95b61_1
-  - intel-openmp=2019.4=233
-  - jpeg=9b=he5867d9_2
-  - jsoncpp=1.8.4=h04f5b5a_0
-  - kiwisolver=1.1.0=py37h0a44026_0
-  - krb5=1.16.1=hddcf347_7
-  - libcurl=7.67.0=h051b688_0
-  - libcxx=4.0.1=hcfea43d_1
-  - libcxxabi=4.0.1=hcfea43d_1
-  - libedit=3.1.20181209=hb402a30_0
-  - libffi=3.2.1=h475c297_4
-  - libgfortran=3.0.1=h93005f0_2
-  - libiconv=1.15=hdd342a3_7
-  - libnetcdf=4.6.1=hd5207e6_2
-  - libogg=1.3.2=h1de35cc_0
-  - libopenblas=0.3.7=hd44dcd8_1
-  - libpng=1.6.37=ha441bb4_0
-  - libssh2=1.8.2=hcdc9a53_2
-  - libtheora=1.1.1=hb4e5f40_1
-  - libtiff=4.1.0=hcb84e12_0
-  - libvorbis=1.3.6=h1de35cc_0
-  - libxml2=2.9.9=hf6e021a_1
-  - libxslt=1.1.33=h33a18ac_0
-  - lxml=4.4.2=py37hef8c89e_0
-  - lz4-c=1.8.1.2=h1de35cc_0
-  - matplotlib=3.1.1=py37h54f8f79_0
-  - matplotlib-base=3.1.1=py37h3a684a6_1
-  - mayavi=4.6.2=py37hdde6e19_4
-  - mkl=2019.4=233
-  - mkl-include=2019.4=233
-  - mkl-service=2.3.0=py37hfbe908c_0
-  - mkl_fft=1.0.15=py37h5e564d8_0
-  - mkl_random=1.1.0=py37ha771720_0
-  - ncurses=6.1=h0a44026_1
-  - numpy=1.17.4=py37h890c691_0
-  - numpy-base=1.17.4=py37h6575580_0
-  - openblas=0.3.7=hd44dcd8_1
-  - openssl=1.1.1h=haf1e3a3_0
-  - pandas=0.25.3=py37h0a44026_0
-  - pcre=8.43=h0a44026_0
-  - pip=19.3.1=py37_0
-  - pyface=6.1.2=py37_0
-  - pygments=2.5.2=py_0
-  - pyparsing=2.4.5=py_0
-  - pyqt=5.9.2=py37h655552a_2
-  - python=3.7.5=h359304d_0
-  - python-dateutil=2.8.1=py_0
-  - python_abi=3.7=1_cp37m
-  - pytz=2019.3=py_0
-  - pyyaml=5.3.1=py37haf1e3a3_1
-  - qt=5.9.7=h468cd18_1
-  - readline=7.0=h1de35cc_5
-  - rhash=1.3.8=ha12b0ac_0
-  - scipy=1.3.1=py37h1410ff5_0
-  - setuptools=42.0.2=py37_0
-  - sip=4.19.8=py37h0a44026_0
-  - six=1.13.0=py37_0
-  - slycot=0.3.5.0=py37h82d0005_0
-  - sqlite=3.30.1=ha441bb4_0
-  - tbb=2019.8=h04f5b5a_0
-  - tk=8.6.8=ha441bb4_0
-  - tornado=6.0.3=py37h1de35cc_0
-  - traits=5.2.0=py37h1de35cc_0
-  - traitsui=6.1.3=py_0
-  - vtk=8.2.0=py37h9bafd54_200
-  - wheel=0.33.6=py37_0
-  - xlrd=1.2.0=py_0
-  - xz=5.2.4=h1de35cc_4
-  - yaml=0.2.5=haf1e3a3_0
-  - zlib=1.2.11=h1de35cc_3
-  - zstd=1.3.7=h5bba6e5_0
-

From 9441349626d03662fde4ee4b56ee1214ced431f4 Mon Sep 17 00:00:00 2001
From: Ben Preston <144227999+ben-l-p@users.noreply.github.com>
Date: Wed, 18 Oct 2023 09:14:19 +0100
Subject: [PATCH 05/15] Changed make version from 3.14 to 3.19 (Apple Silicon
 minimum)

---
 utils/environment_new.yml | 2 +-
 1 file changed, 1 insertion(+), 1 deletion(-)

diff --git a/utils/environment_new.yml b/utils/environment_new.yml
index e16da0afd..f6c7afba7 100644
--- a/utils/environment_new.yml
+++ b/utils/environment_new.yml
@@ -23,4 +23,4 @@ dependencies:
   - xlrd>=1.2.0            
   - python=3.10
   - openpyxl>=3.0.10
-  - cmake=3.14.0
\ No newline at end of file
+  - cmake>=3.19.0

From 6bf9a58569c3217635f1c845622e84d9dd6c1a76 Mon Sep 17 00:00:00 2001
From: Ben Preston <144227999+ben-l-p@users.noreply.github.com>
Date: Wed, 18 Oct 2023 09:19:13 +0100
Subject: [PATCH 06/15] Finalised install guide changes for new environment

---
 docs/source/content/installation.md | 6 ++----
 1 file changed, 2 insertions(+), 4 deletions(-)

diff --git a/docs/source/content/installation.md b/docs/source/content/installation.md
index dbd104c71..96caad405 100644
--- a/docs/source/content/installation.md
+++ b/docs/source/content/installation.md
@@ -72,8 +72,7 @@ or running any SHARPy cases.
     conda install python=3.10
     ```
    
-4. Create the conda environment that SHARPy will use. Change `environment_new.yml` to read `environment_macos.yml`
-   if you are installing SHARPy on MacOS (Intel), or `environment_macos_arm64.yml` if installing on macOS (Apple Silicon).
+4. Create the conda environment that SHARPy will use:
     ```bash
     cd sharpy/utils
     conda env create -f environment_new.yml
@@ -156,8 +155,7 @@ to your taste.
     ```
     This command will check out the `develop` branch and set it to track the remote origin. It will also set the submodules (xbeam and UVLM) to the right commit.
 
-2. Create the conda environment that SHARPy will use. Change `environment_new.yml` to read `environment_macos.yml`
-   if you are installing SHARPy on MacOS (Intel), or `environment_macos_arm64.yml` if installing on macOS (Apple Silicon).
+2. Create the conda environment that SHARPy will use:
     ```bash
     cd sharpy/utils
     conda env create -f environment_new.yml

From f85e81bf555ffaa50bca02ed308b29cc62292a86 Mon Sep 17 00:00:00 2001
From: Ben Preston <144227999+ben-l-p@users.noreply.github.com>
Date: Wed, 18 Oct 2023 12:06:28 +0100
Subject: [PATCH 07/15] Delete utils/environment_macos_arm64.yml

Environment not needed - replaced with environment_new.yml
---
 utils/environment_macos_arm64.yml | 26 --------------------------
 1 file changed, 26 deletions(-)
 delete mode 100644 utils/environment_macos_arm64.yml

diff --git a/utils/environment_macos_arm64.yml b/utils/environment_macos_arm64.yml
deleted file mode 100644
index f2642e411..000000000
--- a/utils/environment_macos_arm64.yml
+++ /dev/null
@@ -1,26 +0,0 @@
-name: sharpy
-channels:
-  - conda-forge
-  - defaults
-dependencies:
-  - asn1crypto>=1.2.0      
-  - colorama>=0.4.1        
-  - control>=0.8.4         
-  - dill>=0.3.1.1          
-  - h5py>=2.9.0            
-  - jupyterlab>=1.2.3      
-  - lxml>=4.4.1            
-  - mayavi>=4.7.1          
-  - nbsphinx>=0.4.3        
-  - pandas>=0.25.3         
-  - pyOpenSSL>=19.0.0      
-  - PySocks>=1.7.1         
-  - PyYAML>=5.1.2          
-  - recommonmark>=0.6.0    
-  - slycot>=0.4.0
-  - sphinx_rtd_theme>=0.4.3
-  - wheel>=0.33.6          
-  - xlrd>=1.2.0            
-  - python=3.10
-  - openpyxl>=3.0.10
-  - cmake>=3.14.0

From bb60716fc4f12707e2f822ef2adb4b0683fef5b4 Mon Sep 17 00:00:00 2001
From: Ben Preston <144227999+ben-l-p@users.noreply.github.com>
Date: Wed, 18 Oct 2023 13:52:43 +0100
Subject: [PATCH 08/15] Delete utils/environment_linux.yml

---
 utils/environment_linux.yml | 170 ------------------------------------
 1 file changed, 170 deletions(-)
 delete mode 100644 utils/environment_linux.yml

diff --git a/utils/environment_linux.yml b/utils/environment_linux.yml
deleted file mode 100644
index 0834869ce..000000000
--- a/utils/environment_linux.yml
+++ /dev/null
@@ -1,170 +0,0 @@
-name: sharpy_env
-channels:
-  - conda-forge
-  - defaults
-dependencies:
-  - _libgcc_mutex=0.1=main
-  - alabaster=0.7.12=py37_0
-  - apptools=4.4.0=py37_1
-  - asn1crypto=1.2.0=py37_0
-  - attrs=19.3.0=py_0
-  - babel=2.7.0=py_0
-  - backcall=0.1.0=py37_0
-  - bleach=3.1.0=py_0
-  - bzip2=1.0.8=h7b6447c_0
-  - ca-certificates=2020.12.5=ha878542_0
-  - certifi=2020.12.5=py37h89c1867_1
-  - cffi=1.13.1=py37h2e261b9_0
-  - chardet=3.0.4=py37_1003
-  - cmake=3.14.0=h52cb24c_0
-  - colorama=0.4.1=py37_0
-  - commonmark=0.9.0=py_0
-  - configobj=5.0.6=py37_1
-  - control=0.8.4=py37h89c1867_0
-  - cryptography=2.8=py37h1ba5d50_0
-  - curl=7.67.0=hbc83047_0
-  - cycler=0.10.0=py37_0
-  - dbus=1.13.12=h746ee38_0
-  - decorator=4.4.1=py_0
-  - defusedxml=0.6.0=py_0
-  - dill=0.3.1.1=py37_0
-  - docutils=0.15.2=py37_0
-  - eigen=3.3.7=hfd86e86_0
-  - entrypoints=0.3=py37_1000
-  - envisage=4.8.0=py_0
-  - expat=2.2.6=he6710b0_0
-  - fontconfig=2.13.0=h9420a91_0
-  - freetype=2.9.1=h8a8886c_1
-  - future=0.18.2=py37_0
-  - glib=2.63.1=h5a9c865_0
-  - gst-plugins-base=1.14.0=hbbd80ab_1
-  - gstreamer=1.14.0=hb453b48_1
-  - h5py=2.9.0=nompi_py37hcafd542_1103
-  - hdf4=4.2.13=h3ca952b_2
-  - hdf5=1.10.4=hb1b8bf9_0
-  - icu=58.2=h9c2bf20_1
-  - idna=2.8=py37_0
-  - imagesize=1.1.0=py37_0
-  - importlib_metadata=0.23=py37_0
-  - intel-openmp=2019.4=243
-  - ipykernel=5.1.3=py37h39e3cac_0
-  - ipython=7.10.1=py37h39e3cac_0
-  - ipython_genutils=0.2.0=py_1
-  - jedi=0.15.1=py37_0
-  - jinja2=2.10.3=py_0
-  - jpeg=9b=h024ee3a_2
-  - json5=0.8.5=py_0
-  - jsoncpp=1.8.4=hfd86e86_0
-  - jsonschema=3.1.1=py37_0
-  - jupyter_client=5.3.3=py37_1
-  - jupyter_core=4.5.0=py_0
-  - jupyterlab=1.2.3=py_0
-  - jupyterlab_server=1.0.6=py_0
-  - kiwisolver=1.1.0=py37he6710b0_0
-  - krb5=1.16.1=h173b8e3_7
-  - lapack=3.6.1=ha44fe06_2
-  - libblas=3.8.0=14_openblas
-  - libcblas=3.8.0=14_openblas
-  - libcurl=7.67.0=h20c2e04_0
-  - libedit=3.1.20181209=hc058e9b_0
-  - libffi=3.2.1=hd88cf55_4
-  - libgcc-ng=9.1.0=hdf63c60_0
-  - libgfortran=3.0.0=1
-  - libgfortran-ng=7.3.0=hdf63c60_0
-  - liblapack=3.8.0=14_openblas
-  - libnetcdf=4.6.1=h11d0813_2
-  - libogg=1.3.2=h7b6447c_0
-  - libopenblas=0.3.7=h5ec1e0e_4
-  - libpng=1.6.37=hbc83047_0
-  - libsodium=1.0.16=h1bed415_0
-  - libssh2=1.8.2=h1ba5d50_0
-  - libstdcxx-ng=9.1.0=hdf63c60_0
-  - libtheora=1.1.1=h5ab3b9f_1
-  - libtiff=4.1.0=h2733197_0
-  - libuuid=1.0.3=h1bed415_2
-  - libvorbis=1.3.6=h7b6447c_0
-  - libxcb=1.13=h1bed415_1
-  - libxml2=2.9.9=hea5a465_1
-  - libxslt=1.1.33=h7d1a2b0_0
-  - lxml=4.4.1=py37hefd8a0e_0
-  - lz4-c=1.8.1.2=h14c3975_0
-  - markupsafe=1.1.1=py37h7b6447c_0
-  - matplotlib=3.1.1=py37h5429711_0
-  - matplotlib-base=3.1.3=py37hef1b27d_0
-  - mayavi=4.7.1=py37h94891b3_2
-  - mistune=0.8.4=py37h516909a_1000
-  - more-itertools=7.2.0=py_0
-  - nbconvert=5.6.1=py37_0
-  - nbformat=4.4.0=py_1
-  - nbsphinx=0.4.3=py_0
-  - ncurses=6.1=he6710b0_1
-  - notebook=6.0.1=py37_0
-  - numpy=1.17.3=py37h95a1406_0
-  - openssl=1.1.1i=h27cfd23_0
-  - packaging=19.2=py_0
-  - pandas=0.25.3=py37hb3f55d8_0
-  - pandoc=2.7.3=0
-  - pandocfilters=1.4.2=py_1
-  - parso=0.5.1=py_0
-  - pcre=8.43=he6710b0_0
-  - pexpect=4.7.0=py37_0
-  - pickleshare=0.7.5=py37_0
-  - pip=19.3.1=py37_0
-  - prometheus_client=0.7.1=py_0
-  - prompt_toolkit=3.0.2=py_0
-  - ptyprocess=0.6.0=py37_0
-  - pycparser=2.19=py37_0
-  - pyface=6.1.2=py37_0
-  - pygments=2.4.2=py_0
-  - pyopenssl=19.0.0=py37_0
-  - pyparsing=2.4.4=py_0
-  - pyqt=5.9.2=py37h05f1152_2
-  - pyrsistent=0.15.5=py37h516909a_0
-  - pysocks=1.7.1=py37_0
-  - python=3.7.5=h0371630_0
-  - python-dateutil=2.8.1=py_0
-  - python_abi=3.7=1_cp37m
-  - pytz=2019.3=py_0
-  - pyyaml=5.1.2=py37h7b6447c_0
-  - pyzmq=18.1.0=py37he6710b0_0
-  - qt=5.9.7=h5867ecd_1
-  - readline=7.0=h7b6447c_5
-  - recommonmark=0.6.0=py_0
-  - requests=2.22.0=py37_0
-  - rhash=1.3.8=h1ba5d50_0
-  - scipy=1.3.2=py37h921218d_0
-  - send2trash=1.5.0=py37_0
-  - setuptools=41.6.0=py37_0
-  - sip=4.19.8=py37hf484d3e_0
-  - six=1.13.0=py37_0
-  - snowballstemmer=2.0.0=py_0
-  - sphinx=3.0.3=py_0
-  - sphinx_rtd_theme=0.5.0=pyh9f0ad1d_0
-  - sphinxcontrib-applehelp=1.0.1=py_0
-  - sphinxcontrib-devhelp=1.0.1=py_0
-  - sphinxcontrib-htmlhelp=1.0.2=py_0
-  - sphinxcontrib-jsmath=1.0.1=py_0
-  - sphinxcontrib-qthelp=1.0.2=py_0
-  - sphinxcontrib-serializinghtml=1.1.3=py_0
-  - sqlite=3.30.1=h7b6447c_0
-  - tbb=2019.8=hfd86e86_0
-  - terminado=0.8.3=py37_0
-  - testpath=0.4.4=py_0
-  - tk=8.6.8=hbc83047_0
-  - tornado=6.0.3=py37h7b6447c_0
-  - traitlets=4.3.3=py37_0
-  - traits=5.2.0=py37h7b6447c_0
-  - traitsui=6.1.3=py_0
-  - urllib3=1.24.2=py37_0
-  - vtk=8.2.0=py37haa4764d_200
-  - wcwidth=0.1.7=py37_0
-  - webencodings=0.5.1=py_1
-  - wheel=0.33.6=py37_0
-  - xlrd=1.2.0=py37_0
-  - xz=5.2.4=h14c3975_4
-  - yaml=0.1.7=had09818_2
-  - zeromq=4.3.1=he6710b0_3
-  - zipp=0.6.0=py_0
-  - zlib=1.2.11=h7b6447c_3
-  - zstd=1.3.7=h0b5b093_0
-  - slycot=0.4.0.0=py37h27181d0_1

From 044064607e966c1bda17d8de883ea48373e8c662 Mon Sep 17 00:00:00 2001
From: Ben Preston <144227999+ben-l-p@users.noreply.github.com>
Date: Wed, 18 Oct 2023 13:52:56 +0100
Subject: [PATCH 09/15] Delete utils/environment_minimal.yml

---
 utils/environment_minimal.yml | 104 ----------------------------------
 1 file changed, 104 deletions(-)
 delete mode 100644 utils/environment_minimal.yml

diff --git a/utils/environment_minimal.yml b/utils/environment_minimal.yml
deleted file mode 100644
index ea5841579..000000000
--- a/utils/environment_minimal.yml
+++ /dev/null
@@ -1,104 +0,0 @@
-name: sharpy_minimal
-channels:
-  - conda-forge
-  - defaults
-dependencies:
-  - _libgcc_mutex=0.1=main
-  - apptools=4.5.0=py_0
-  - bzip2=1.0.8=h7b6447c_0
-  - ca-certificates=2020.12.5=ha878542_0
-  - certifi=2020.12.5=py37h89c1867_1
-  - cmake=3.14.0=h52cb24c_0
-  - colorama=0.4.1=py37_0
-  - configobj=5.0.6=py_0
-  - control=0.8.4=py37h89c1867_0
-  - curl=7.67.0=hbc83047_0
-  - cycler=0.10.0=py_2
-  - dbus=1.13.6=he372182_0
-  - dill=0.3.1.1=py37_0
-  - eigen=3.3.7=hc9558a2_1001
-  - envisage=4.8.0=py_0
-  - expat=2.2.6=he6710b0_0
-  - fontconfig=2.13.1=he4413a7_1000
-  - freetype=2.10.0=he983fc9_1
-  - future=0.18.2=py37_0
-  - gettext=0.19.8.1=hc5be6a0_1002
-  - glib=2.58.3=py37h6f030ca_1002
-  - gst-plugins-base=1.14.5=h0935bb2_0
-  - gstreamer=1.14.5=h36ae1b5_0
-  - h5py=2.9.0=py37h7918eee_0
-  - hdf4=4.2.13=h3ca952b_2
-  - hdf5=1.10.4=hb1b8bf9_0
-  - icu=58.2=hf484d3e_1000
-  - jpeg=9c=h14c3975_1001
-  - jsoncpp=1.8.4=hfd86e86_0
-  - kiwisolver=1.1.0=py37hc9558a2_0
-  - krb5=1.16.1=h173b8e3_7
-  - lapack=3.6.1=ha44fe06_2
-  - libblas=3.8.0=14_openblas
-  - libcblas=3.8.0=14_openblas
-  - libcurl=7.67.0=h20c2e04_0
-  - libedit=3.1.20181209=hc058e9b_0
-  - libffi=3.2.1=hd88cf55_4
-  - libgcc-ng=9.1.0=hdf63c60_0
-  - libgfortran=3.0.0=1
-  - libgfortran-ng=7.3.0=hdf63c60_2
-  - libiconv=1.15=h516909a_1005
-  - liblapack=3.8.0=14_openblas
-  - libnetcdf=4.6.1=h11d0813_2
-  - libogg=1.3.2=h7b6447c_0
-  - libopenblas=0.3.7=h5ec1e0e_4
-  - libpng=1.6.37=hed695b0_0
-  - libssh2=1.8.2=h1ba5d50_0
-  - libstdcxx-ng=9.1.0=hdf63c60_0
-  - libtheora=1.1.1=h5ab3b9f_1
-  - libtiff=4.1.0=h2733197_0
-  - libuuid=2.32.1=h14c3975_1000
-  - libvorbis=1.3.6=h7b6447c_0
-  - libxcb=1.13=h14c3975_1002
-  - libxml2=2.9.9=hea5a465_1
-  - libxslt=1.1.33=h7d1a2b0_0
-  - lxml=4.4.2=py37hefd8a0e_0
-  - lz4-c=1.8.1.2=h14c3975_0
-  - matplotlib=3.1.1=py37h5429711_0
-  - matplotlib-base=3.1.3=py37hef1b27d_0
-  - mayavi=4.7.1=py37h94891b3_2
-  - ncurses=6.1=he6710b0_1
-  - numpy=1.17.3=py37h95a1406_0
-  - openssl=1.1.1i=h27cfd23_0
-  - pandas=0.25.3=py37hb3f55d8_0
-  - pcre=8.43=he1b5a44_0
-  - pip=19.3.1=py37_0
-  - pthread-stubs=0.4=h14c3975_1001
-  - pyface=6.1.2=py37_0
-  - pygments=2.5.2=py_0
-  - pyparsing=2.4.5=py_0
-  - pyqt=5.9.2=py37hcca6a23_4
-  - python=3.7.5=h0371630_0
-  - python-dateutil=2.8.1=py_0
-  - python_abi=3.7=1_cp37m
-  - pytz=2019.3=py_0
-  - pyyaml=5.1.2=py37h7b6447c_0
-  - qt=5.9.7=h52cfd70_2
-  - readline=7.0=h7b6447c_5
-  - rhash=1.3.8=h1ba5d50_0
-  - scipy=1.3.2=py37h921218d_0
-  - setuptools=42.0.2=py37_0
-  - sip=4.19.8=py37hf484d3e_0
-  - six=1.13.0=py37_0
-  - slycot=0.4.0.0=py37h27181d0_1
-  - sqlite=3.30.1=h7b6447c_0
-  - tbb=2019.8=hfd86e86_0
-  - tk=8.6.8=hbc83047_0
-  - tornado=6.0.3=py37h516909a_0
-  - traits=5.2.0=py37h7b6447c_0
-  - traitsui=6.1.3=py_0
-  - vtk=8.2.0=py37haa4764d_200
-  - wheel=0.33.6=py37_0
-  - xlrd=1.2.0=py37_0
-  - xorg-libxau=1.0.9=h14c3975_0
-  - xorg-libxdmcp=1.1.3=h516909a_0
-  - xz=5.2.4=h14c3975_4
-  - yaml=0.1.7=had09818_2
-  - zlib=1.2.11=h7b6447c_3
-  - zstd=1.3.7=h0b5b093_0

From 0493bfd0fb3461d495f092320ea3b506192f5bfb Mon Sep 17 00:00:00 2001
From: Ben Preston <144227999+ben-l-p@users.noreply.github.com>
Date: Wed, 18 Oct 2023 13:53:41 +0100
Subject: [PATCH 10/15] Rename environment_new.yml to environment.yml

---
 utils/{environment_new.yml => environment.yml} | 0
 1 file changed, 0 insertions(+), 0 deletions(-)
 rename utils/{environment_new.yml => environment.yml} (100%)

diff --git a/utils/environment_new.yml b/utils/environment.yml
similarity index 100%
rename from utils/environment_new.yml
rename to utils/environment.yml

From aace787862880dcf072ea3dda6d6cd7c04e3f52c Mon Sep 17 00:00:00 2001
From: Ben Preston <144227999+ben-l-p@users.noreply.github.com>
Date: Wed, 18 Oct 2023 13:55:58 +0100
Subject: [PATCH 11/15] Update bashrc to not use minimal environment

---
 utils/docker/bashrc | 2 +-
 1 file changed, 1 insertion(+), 1 deletion(-)

diff --git a/utils/docker/bashrc b/utils/docker/bashrc
index aaf5aee1c..dbe250efe 100644
--- a/utils/docker/bashrc
+++ b/utils/docker/bashrc
@@ -26,7 +26,7 @@ fi
 unset __conda_setup
 # <<< conda initialize <<<
 
-conda activate sharpy_minimal
+conda activate sharpy
 
 # custom prompt
 PS1="SHARPy> "

From d1760e2b8c10cb7f40f5daebe92daa5f743f59e8 Mon Sep 17 00:00:00 2001
From: Ben Preston <144227999+ben-l-p@users.noreply.github.com>
Date: Wed, 18 Oct 2023 13:59:02 +0100
Subject: [PATCH 12/15] Renamed environment file in documentation

---
 docs/source/content/installation.md | 8 +++-----
 1 file changed, 3 insertions(+), 5 deletions(-)

diff --git a/docs/source/content/installation.md b/docs/source/content/installation.md
index 96caad405..a3f6d6741 100644
--- a/docs/source/content/installation.md
+++ b/docs/source/content/installation.md
@@ -75,12 +75,10 @@ or running any SHARPy cases.
 4. Create the conda environment that SHARPy will use:
     ```bash
     cd sharpy/utils
-    conda env create -f environment_new.yml
+    conda env create -f environment.yml
     cd ../..
     ```
-    This should take approximately 15 minutes to complete (Tested on Ubuntu 22.04.1). We also provide a 
-    lightweight environment with the minimum required dependencies. If you'd like to use it, create the 
-    conda environment using `environment_minimal.yml`.
+    This should take approximately 15 minutes to complete (Tested on Ubuntu 22.04.1). 
 
 5. Activate the `sharpy` conda environment:
     ```bash
@@ -158,7 +156,7 @@ to your taste.
 2. Create the conda environment that SHARPy will use:
     ```bash
     cd sharpy/utils
-    conda env create -f environment_new.yml
+    conda env create -f environment.yml
     cd ../..
     ```
 

From 2995b061133f37ef243c8443dcb18a6aad39380b Mon Sep 17 00:00:00 2001
From: Ben Preston <144227999+ben-l-p@users.noreply.github.com>
Date: Wed, 18 Oct 2023 14:26:25 +0100
Subject: [PATCH 13/15] Update Dockerfile to use renamed environment

---
 Dockerfile | 2 +-
 1 file changed, 1 insertion(+), 1 deletion(-)

diff --git a/Dockerfile b/Dockerfile
index 9f49d0448..c3e8e2ff6 100644
--- a/Dockerfile
+++ b/Dockerfile
@@ -31,7 +31,7 @@ RUN conda init bash && \
     conda config --set always_yes yes --set changeps1 no && \
     conda update -q conda && \
     conda config --set auto_activate_base false && \
-    conda env create -f /sharpy_dir/utils/environment_minimal.yml && conda clean -afy && \
+    conda env create -f /sharpy_dir/utils/environment.yml && conda clean -afy && \
     find /miniconda3/ -follow -type f -name '*.a' -delete && \
     find /miniconda3/ -follow -type f -name '*.pyc' -delete && \
     find /miniconda3/ -follow -type f -name '*.js.map' -delete

From 5034646d287ce6766a2fa5d2b6290be702e20001 Mon Sep 17 00:00:00 2001
From: Ben Preston <144227999+ben-l-p@users.noreply.github.com>
Date: Wed, 18 Oct 2023 14:27:45 +0100
Subject: [PATCH 14/15] Update sharpy_tests.yaml to use renamed environment

---
 .github/workflows/sharpy_tests.yaml | 2 +-
 1 file changed, 1 insertion(+), 1 deletion(-)

diff --git a/.github/workflows/sharpy_tests.yaml b/.github/workflows/sharpy_tests.yaml
index 6945cc94d..d5dff4462 100644
--- a/.github/workflows/sharpy_tests.yaml
+++ b/.github/workflows/sharpy_tests.yaml
@@ -51,7 +51,7 @@ jobs:
           hash -r
           export QT_QPA_PLATFORM='offscreen'
           sudo apt install libeigen3-dev
-          conda env create -f utils/environment_new.yml
+          conda env create -f utils/environment.yml
           conda init bash
           source activate sharpy
           git submodule init

From 0b343d87bf231d636630fc7ce96f816e51d86244 Mon Sep 17 00:00:00 2001
From: Ben Preston <144227999+ben-l-p@users.noreply.github.com>
Date: Wed, 18 Oct 2023 14:28:59 +0100
Subject: [PATCH 15/15] Update contributing.md to use renamed environment

---
 docs/source/content/contributing.md | 2 +-
 1 file changed, 1 insertion(+), 1 deletion(-)

diff --git a/docs/source/content/contributing.md b/docs/source/content/contributing.md
index 92caf694a..3734a3086 100644
--- a/docs/source/content/contributing.md
+++ b/docs/source/content/contributing.md
@@ -11,7 +11,7 @@ If you are submitting a bug report:
 same branch.
 
 2. Double check that your python distribution is updated by comparing with 
-the `utils/environment_*.yml` file.
+the `utils/environment.yml` file.
 
 3. Try to assemble a minimal working example that can be run quickly and easily.