Development

docs/README.md

@@ -56,6 +56,14 @@ from scratch.
 If you plan to do Python programming in a Linux or HPC environment you should
 be familiar with these as well.
 
+For following along hands-on, you need
+* laptop or desktop with internet access.
+* a system set up so you can connect to an HPC system, an account on an HPC
+  system (e.g., VSC, CECI, ...), compute credits if that is required to run
+  jobs on the HPC system if you want to use an HPC system;
+* a Python environment that can run Jupyter Lab if you want to use your own system;
+* access to Google Colaboratory if you prefer not to install software.
+
 
 ## Level
 

docs/_config.yml

@@ -1 +1,2 @@
-theme: jekyll-theme-slate
+title: "Scientific Python"
+theme: jekyll-theme-slate

environment.yml

@@ -3,7 +3,6 @@ channels:
   - conda-forge
 dependencies:
   - bokeh
-  - hdf5
   - ipywidgets
   - jupyterlab
   - jupyterlab_widgets
@@ -14,334 +13,13 @@ dependencies:
   - opencv
   - pandas
   - pytables
-  - python
-  - scikit-image
+  - h5py
   - scipy
+  - scikit-image
   - sympy
   - xarray
-  - debugpy
-  - nbclassic
-  - pygments
-  - ipython
-  - libllvm11
-  - openh264
-  - libwebp
-  - cycler
-  - lerc
-  - mock
-  - pyqt
-  - blas
-  - xorg-libxau
-  - notebook-shim
-  - stack_data
-  - backcall
-  - libgcc-ng
-  - entrypoints
-  - jxrlib
-  - argon2-cffi-bindings
-  - appdirs
-  - libtasn1
-  - libsodium
-  - bzip2
-  - fonttools
-  - libbrotlidec
-  - jupyter_core
-  - libunistring
-  - pyqt5-sip
-  - comm
-  - tzdata
-  - mpfr
-  - partd
-  - libtiff
-  - libopencv
-  - libgomp
-  - libbrotlienc
-  - pure_eval
-  - xorg-fixesproto
-  - jsonschema
-  - pyparsing
-  - brotli
-  - libopus
-  - nbformat
-  - send2trash
-  - libblas
-  - glib-tools
-  - python-fastjsonschema
-  - fontconfig
-  - pytz
-  - openssl
-  - dask-core
-  - yaml
-  - dbus
-  - idna
-  - libglu
-  - matplotlib-base
-  - pyrsistent
-  - typing_extensions
-  - libogg
-  - xorg-libxext
-  - gnutls
-  - charset-normalizer
-  - contourpy
-  - pyqt-impl
-  - xorg-xextproto
-  - libglib
-  - notebook
   - networkx
-  - freeglut
-  - tomli
-  - ffmpeg
-  - expat
-  - libopenblas
-  - libzopfli
-  - libgfortran-ng
-  - attrs
-  - traitlets
-  - imagecodecs
-  - sqlite
-  - openjpeg
-  - munkres
-  - libxslt
-  - giflib
-  - wheel
-  - libcurl
-  - markupsafe
-  - python_abi
-  - pooch
-  - gettext
-  - krb5
-  - requests
-  - pywavelets
-  - cairo
-  - cfitsio
-  - pillow
-  - py-opencv
-  - terminado
-  - certifi
-  - xorg-libxfixes
-  - qt
-  - alsa-lib
-  - pickleshare
-  - libcblas
-  - websocket-client
-  - locket
-  - bleach
-  - libaec
-  - nest-asyncio
-  - jasper
-  - kiwisolver
-  - libstdcxx-ng
-  - libdeflate
-  - argon2-cffi
-  - libidn2
-  - xorg-kbproto
-  - pyyaml
-  - _openmp_mutex
-  - prometheus_client
-  - jpeg
-  - widgetsnbextension
-  - asttokens
-  - libxml2
-  - six
-  - packaging
-  - cffi
-  - c-ares
-  - libedit
-  - libevent
-  - python-dateutil
-  - brotli-bin
-  - pyzmq
-  - executing
-  - readline
-  - libssh2
-  - libffi
-  - platformdirs
-  - mysql-common
-  - mpc
-  - ptyprocess
-  - libclang
-  - libpng
-  - _libgcc_mutex
-  - jupyterlab_pygments
-  - mpmath
-  - jupyterlab_server
-  - pexpect
-  - matplotlib-inline
-  - babel
-  - graphite2
-  - glib
-  - zeromq
-  - lame
-  - xorg-libxi
-  - tornado
-  - pysocks
-  - ca-certificates
-  - jinja2
-  - setuptools
-  - icu
-  - libxcb
-  - blosc
-  - x264
-  - lz4-c
-  - pyopenssl
-  - decorator
-  - harfbuzz
-  - libuv
-  - gstreamer
-  - ld_impl_linux-64
-  - soupsieve
-  - ipykernel
-  - nss
-  - libzlib
-  - fsspec
-  - zlib
-  - imageio
-  - pcre
-  - cytoolz
-  - mysql-libs
-  - brotlipy
-  - libprotobuf
-  - cryptography
-  - cloudpickle
-  - gst-plugins-base
-  - xorg-xproto
-  - xyzservices
-  - brunsli
-  - tifffile
-  - jupyter_client
-  - lxml
-  - lcms2
-  - pandocfilters
-  - libuuid
-  - psutil
-  - libxkbcommon
-  - beautifulsoup4
-  - defusedxml
-  - flit-core
-  - libiconv
-  - prompt-toolkit
-  - gmp
-  - jedi
-  - wcwidth
-  - snappy
-  - libbrotlicommon
-  - nettle
-  - charls
-  - pixman
-  - pyqtwebengine
-  - tk
-  - mistune
-  - ipython_genutils
-  - nspr
   - nbconvert
-  - xz
-  - webencodings
-  - zfp
-  - sniffio
-  - anyio
-  - lzo
-  - liblapacke
-  - libgfortran5
-  - pyqtchart
-  - ncurses
-  - liblapack
-  - libwebp-base
-  - parso
-  - bottleneck
-  - libvorbis
-  - pycparser
-  - pip
-  - freetype
-  - gmpy2
-  - json5
-  - zstd
-  - jupyter_server
-  - libpq
-  - nbclient
-  - libnghttp2
-  - libev
-  - toolz
-  - urllib3
-  - tinycss2
-  - numpy-base
-  - xorg-inputproto
-  - xorg-libx11
-  - typing-extensions
-  - jupyter_events
-  - python-tzdata
-  - exceptiongroup
-  - pcre2
-  - rfc3986-validator
-  - nbconvert-core
-  - libexpat
-  - c-blosc2
-  - overrides
-  - backports.functools_lru_cache
-  - prompt_toolkit
-  - zipp
-  - nomkl
-  - libavif
-  - typing_utils
-  - unicodedata2
-  - async-lru
-  - pandoc
-  - rfc3339-validator
-  - lazy_loader
-  - libsqlite
-  - aom
-  - nbconvert-pandoc
-  - importlib-metadata
-  - zlib-ng
-  - importlib_resources
-  - jupyter_server_terminals
-  - backports
-  - jupyter-lsp
-  - importlib_metadata
-  - click
-  - python-json-logger
-  - dav1d
-  - h2
-  - arrow
-  - cached_property
-  - isoduration
-  - rpds-py
-  - httpcore
-  - types-python-dateutil
-  - webcolors
-  - referencing
-  - pkgutil-resolve-name
-  - jsonschema-specifications
-  - hyperframe
-  - libasprintf
-  - jsonschema-with-format-nongpl
-  - libgettextpo
-  - gettext-tools
-  - libasprintf-devel
-  - cached-property
-  - fqdn
-  - jsonpointer
-  - httpx
-  - uri-template
-  - h11
-  - hpack
-  - brotli-python
-  - libgettextpo-devel
-  - h5py
-  - libgfortran
-  - zstandard
-  - pthread-stubs
-  - libdrm
-  - libstdcxx
-  - lazy-loader
-  - xorg-libxxf86vm
-  - libglvnd
-  - libgl
-  - libpciaccess
-  - xorg-libxdamage
-  - xorg-xorgproto
-  - libegl
-  - xorg-libxdmcp
-  - libglx
-  - libgcc
-  - qhull
+  - nbdime
+  - seaborn
 prefix: /home/gjb/mambaforge/envs/scientific_python