datahub-user-image/environment.yml at main · berkeley-dsep-infra/datahub-user-image · GitHub

1
2
3
4
5
6
7
8
9
10
11
12
13
14
15
16
17
18
19
20
21
22
23
24
25
26
27
28
29
30
31
32
33
34
35
36
37
38
39
40
41
42
43
44
45
46
47
48
49
50
51
52
53
54
55
56
57
58
59
60
61
62
63
64
65
66
67
68
69
70
71
72
73
74
75
76
77
78
79
80
81
82
83
84
85
86
87
88
89
90
91
92
93
94
95
96
97
98
99
100
101
102
103
104
105
106
107
108
109
110
111
112
113
114
115
116
117
118
119
120
121
122
123
124
125
126
127
128
129
130
131
132
133
134
135
136
137
138
139
140
141
142
143
144
145
146
147
148
149
150
151
152
153
154
155
156
157
158
159
160
161
162
163
164
165
166
167
168
169
170
171
172
173
174
175
176
177
178
179
180
181
182
183
184
185
186
name: datahub
# This is the standard conda configuration file. Use this file to list
# the conda packages that you need installed in your environment.
channels:
  - conda-forge

dependencies:
  # Items required for basic level functionality
  - gh-scoped-creds==4.1
  - git==2.49.0
  - jupyter-archive==3.4.0
  - jupyter-offlinenotebook==0.3.1
  - jupyter-resource-usage==1.1.1
  - jupyter-server-proxy==4.4.0
  - jupyter_server==2.16.0
  - jupyterhub==5.3.0
  - jupyterlab==4.4.3
  - jupyterlab-git==0.51.1
  - jupyterlab_rise==0.43.1
  - jupytext==1.17.1
  - nbgitpuller==1.2.2
  - notebook==7.4.3
  - otter-grader==6.1.3
  - pip==25.1.1
  - python==3.11.*
  - sqlite>=3.40
  - libsqlite>=3.40

  # other packages
  #- nodejs=18.*
  - appmode==1.0.0
  - ipykernel = 6.29.5
  - ipywidgets==8.1.5
  - jupyterlab-geojson==3.4.0
  - jupyter-rsession-proxy==2.2.1
  - jupyter-syncthing-proxy==1.0.3
  - nbclassic==1.0.0
  - requests==2.32.3
  - syncthing==1.29.2
  - traitlets=5.14.3

  # vscode
  - jupyter-vscode-proxy==0.6
  - code-server==4.96.2

  # jupyterbook
  - mystmd==1.3.19

  # Base scientific packages that other conda packages we install depend on
  # We don't want to have conda packages depend on pip packages if possible
  - decorator=5.1.1
  - ipympl=0.9.*
  - matplotlib=3.10.*
  - networkx=3.4.2
  - nltk=3.9.1
  - numpy=2.2.*
  - pandas==2.2.3
  - scikit-learn=1.6.0
  - scipy=1.14.1
  - seaborn=0.13.2
  - spacy==3.8.2
  - statsmodels=0.14.4

  # [DH-384], L&S 22, Fall 2024
  # Packages listed below will be used during SP 25
  - typing_extensions==4.12.2
  - spacy-model-en_core_web_sm=3.8.0
  - spacy-model-en_core_web_md=3.8.0

  # ls 88-3; neuro
  - pillow=11.1.0

  # modules
  - beautifulsoup4==4.12.3

  # PS88, Fall '21 and "future iterations of the class."
  # https://github.com/berkeley-dsep-infra/datahub/issues/2925
  - linearmodels==6.1

  # INDENG 142 Spring 2021 (future semesters as well) - https://github.com/berkeley-dsep-infra/datahub/issues/2314
  - fancyimpute==0.7.0

  # 2024-08 workshop, #5908
  - tree==2.2.1
  - ruff==0.8.5

  # Stat 165/265 requires prophet, Spring, 2024
  - prophet==1.1.6

  # ENERES 131, Fall '24 and "Fall semesters for the foreseeable future"
  # [DH-364] https://github.com/berkeley-dsep-infra/datahub/issues/6155
  - openpyxl==3.1.5
  # [DH-393] https://github.com/berkeley-dsep-infra/datahub/issues/6346
  - pyogrio==0.10.0

  # Google spreadsheets, Eric Van Dusen / Keeley Takimoto / Modules
  - gspread-pandas==2.2.3
  - gspread==5.12.4

  # issue #929, SW 282 - fall 2019
  # sknapp 2024-08-12:  keeping this package as i believe it's still useful
  - pyreadstat==1.2.8

  # issue 954, EPS24 - fall 2019
  # sknapp 2024-08-12:  keeping this package as i believe it's still useful
  - xarray==2025.1.1

  # issue 1847; LS 22 spring 2021; "likely will need it yearly"
  - python-graphviz==0.20.3

  # [DH-243] https://github.com/berkeley-dsep-infra/datahub/issues/5571, Legal Studies 123, Spring 24; each Spring
  - geopandas==1.1.1
  - rtree==1.3.0

  # sknapp 2023-12-15:  we will eventually move prob140 back to datahub in FA24
  # https://jira-secure.berkeley.edu/browse/DH-203
  - sympy==1.13.3

  # eps 109; fall 2019
  # sknapp 2024-08-12:  keeping this package as i believe it's still useful
  - ffmpeg-python==0.2.0

  # issue #875, global 150Q/pacs 190 - fall 2019
  # sknapp 2024-08-12:  keeping this package as i believe it's still useful
  - wordcloud==1.9.4

  # https://github.com/berkeley-dsep-infra/datahub/issues/2950
  # Needed to work with a new enough version of httplib2
  - httplib2==0.22.0

  # Engineering 7 https://github.com/berkeley-dsep-infra/datahub/issues/5337
  - pydantic==2.10.5

  # Econ 148, https://github.com/berkeley-dsep-infra/datahub/issues/6791
  - jupysql==0.10.17

  # Econ 148; Spring 2025; https://github.com/berkeley-dsep-infra/datahub/issues/6872
  - lifelines==0.30.0

  # French 80, Fall 2025; https://github.com/berkeley-dsep-infra/datahub/issues/7501
  - geojson==3.2.0
  - pyproj==3.7.2

  # DH-654, Make git-credentials-helper work for ds4bio course
  - pyjwt==2.10.1

  - pip:
    - git-credential-helpers==0.2
    - jupyter-shiny-proxy==1.3.0
    - nbconvert[webpdf]==7.16.6

    # Measure popularity of different packages in our hubs
    # https://discourse.jupyter.org/t/request-for-implementation-instrument-libraries-actively-used-by-users-on-a-jupyterhub/7994?u=yuvipanda
    - git+https://github.com/shaneknapp/python-popularity-contest.git@add-error-handling

    # Econ 148, Spring 2023 https://github.com/berkeley-dsep-infra/datahub/issues/4093
    - pycountry-convert==0.7.2

    # sknapp 2023-12-15:  we will eventually move prob140 back to datahub in FA24
    # https://jira-secure.berkeley.edu/browse/DH-203
    - prob140==0.4.1.6

    # https://github.com/berkeley-dsep-infra/datahub/issues/5497
    - ottr-force-save-labextension==0.1.1

    # [DH-540], Physics 77/88, Fall 2025
    - otter-grader-labextension==0.1.1

    # [DH-319] https://github.com/berkeley-dsep-infra/datahub/issues/5827, ESPM 157
    - ibis-framework[pandas,duckdb]==9.2.0

    # [DH-384], L&S 22, Fall 2024
    # The 0.2.2 conda-forge package is 3y old as of 2025-01 and cannot be
    # installed with newer numpy.
    - lemminflect==0.2.3

    # [DH-557], Data Courses, Fall 2025
    - datascience==0.18.0

    # Adding a11y-checker package to datahub image since it is required for demoing the extension in workshop hub to non Berkeley folks
    - jupyterlab-a11y-checker==0.2.2

    # [DH-488], Legal Studies 123, https://github.com/berkeley-dsep-infra/datahub/issues/6964
    - gensim==4.4.0

    # ATTEMPT TO PUT NEW PACKAGES IN THE CONDA LIST ABOVE FIRST, RATHER THAN PIP