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baakaani commited on
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0067f64
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1 Parent(s): fd151fa

updating github actions

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Files changed (1) hide show
  1. .github/workflows/test_gedi.yml +92 -75
.github/workflows/test_gedi.yml CHANGED
@@ -12,23 +12,23 @@ jobs:
12
  test_feature-extraction:
13
  runs-on: ubuntu-latest
14
 
 
15
  steps:
16
  - name: Checkout code
17
  uses: actions/checkout@v4
18
 
19
- - name: Install Miniconda
20
- uses: conda-incubator/setup-miniconda@v2
 
 
21
 
22
- - name: Create conda environment
23
- run: conda env create -f .conda.yml
24
-
25
- - name: Activate conda environment
26
- run: echo "conda activate gedi" >> $GITHUB_ENV
27
- shell: bash
28
 
29
  - name: Run test
30
- run: |
31
- conda activate gedi
32
  python main.py -o config_files/options/baseline.json -a config_files/algorithm/pipeline_steps/feature_extraction.json
33
 
34
  - name: Compare output
@@ -38,58 +38,65 @@ jobs:
38
  test_generation:
39
  runs-on: ubuntu-latest
40
 
 
41
  steps:
42
  - name: Checkout code
43
  uses: actions/checkout@v4
44
 
45
- - name: Install Miniconda
46
- uses: conda-incubator/setup-miniconda@v2
 
 
47
 
48
- - name: Create conda environment
49
- run: conda env create -f .conda.yml
 
50
 
51
- - name: Activate conda environment
52
- run: echo "conda activate gedi" >> $GITHUB_ENV
53
- shell: bash
 
54
 
55
  - name: Run test
56
- run: |
57
- conda activate gedi
58
  python main.py -o config_files/options/baseline.json -a config_files/algorithm/pipeline_steps/generation.json
59
 
60
  - name: Compare output 1
61
- run: diff data/validation/genELexperiment2_07_04.json output/features/grid_feat/2_enself_rt20v/genELexperiment2_07_04.json
 
62
 
63
  - name: Compare output 2
64
- run: diff data/validation/genELexperiment1_04_02.json output/features/grid_feat/2_enself_rt20v/genELexperiment1_04_02.json
 
65
 
66
  - name: Compare output 3
67
- run: diff data/validation/genELexperiment3_04.json output/features/grid_feat/1_enself/genELexperiment3_04.json
 
68
 
69
  - name: Compare output 4
70
- run: diff data/validation/genELexperiment4_02.json output/features/grid_feat/1_rt20v/genELexperiment4_02.json
71
-
72
 
73
  test_benchmark:
74
  runs-on: ubuntu-latest
75
 
 
76
  steps:
77
  - name: Checkout code
78
  uses: actions/checkout@v4
79
 
80
- - name: Install Miniconda
81
- uses: conda-incubator/setup-miniconda@v2
 
 
82
 
83
- - name: Create conda environment
84
- run: conda env create -f .conda.yml
85
-
86
- - name: Activate conda environment
87
- run: echo "conda activate gedi" >> $GITHUB_ENV
88
- shell: bash
89
 
90
  - name: Run test
91
- run: |
92
- conda activate gedi
93
  python main.py -o config_files/options/baseline.json -a config_files/algorithm/pipeline_steps/benchmark.json
94
 
95
  - name: Convert output and validation to same encoding
@@ -102,96 +109,106 @@ jobs:
102
  test_augmentation:
103
  runs-on: ubuntu-latest
104
 
 
105
  steps:
106
  - name: Checkout code
107
  uses: actions/checkout@v4
108
 
109
- - name: Install Miniconda
110
- uses: conda-incubator/setup-miniconda@v2
 
 
111
 
112
- - name: Create conda environment
113
- run: conda env create -f .conda.yml
114
-
115
- - name: Activate conda environment
116
- run: echo "conda activate gedi" >> $GITHUB_ENV
117
- shell: bash
118
 
119
  - name: Run test
120
- run: |
121
- conda activate gedi
122
  python main.py -o config_files/options/baseline.json -a config_files/algorithm/pipeline_steps/augmentation.json
123
 
124
-
125
  test_evaluation-plotter:
126
  runs-on: ubuntu-latest
127
 
 
128
  steps:
129
  - name: Checkout code
130
  uses: actions/checkout@v4
131
 
132
- - name: Install Miniconda
133
- uses: conda-incubator/setup-miniconda@v2
 
 
134
 
135
- - name: Create conda environment
136
- run: conda env create -f .conda.yml
 
137
 
138
- - name: Activate conda environment
139
- run: echo "conda activate gedi" >> $GITHUB_ENV
140
- shell: bash
 
141
 
142
  - name: Run test
143
- run: |
144
- conda activate gedi
145
- python main.py -o config_files/options/baseline.json -a config_files/algorithm/pipeline_steps/evaluation_plotter.json
146
 
 
147
 
148
  test_integration:
149
  runs-on: ubuntu-latest
150
 
 
151
  steps:
152
  - name: Checkout code
153
  uses: actions/checkout@v4
154
 
155
- - name: Install Miniconda
156
- uses: conda-incubator/setup-miniconda@v2
 
 
157
 
158
- - name: Create conda environment
159
- run: conda env create -f .conda.yml
 
160
 
161
- - name: Activate conda environment
162
- run: echo "conda activate gedi" >> $GITHUB_ENV
163
- shell: bash
 
164
 
165
  - name: Run test
166
- run: |
167
- conda activate gedi
168
  python main.py -o config_files/options/baseline.json -a config_files/algorithm/experiment_test.json
169
 
170
-
171
  test_grid_experiments_script:
172
  runs-on: ubuntu-latest
173
 
 
174
  steps:
175
  - name: Checkout code
176
  uses: actions/checkout@v4
177
 
178
- - name: Install Miniconda
179
- uses: conda-incubator/setup-miniconda@v2
 
 
180
 
181
- - name: Create conda environment
182
- run: conda env create -f .conda.yml
 
183
 
184
- - name: Activate conda environment
185
- run: echo "conda activate gedi" >> $GITHUB_ENV
186
- shell: bash
 
187
 
188
  - name: Run test
189
- run: |
190
- conda activate gedi
191
  python execute_grid_experiments.py config_files/algorithm/test
192
 
193
  - name: Convert output and validation to same encoding
194
  run: iconv -f UTF-8 -t ASCII output/features/generated/2_bpic_features/2_ense_enseef_feat.csv > data/validation/2_ense_enseef_feat.csv
195
 
196
  - name: Compare output
197
- run: diff data/validation/2_ense_enseef_feat.csv output/features/generated/2_bpic_features/2_ense_enseef_feat.csv
 
12
  test_feature-extraction:
13
  runs-on: ubuntu-latest
14
 
15
+ # Setting up a python envronment for the test script to run
16
  steps:
17
  - name: Checkout code
18
  uses: actions/checkout@v4
19
 
20
+ - name: Set up Python
21
+ uses: actions/setup-python@v5
22
+ with:
23
+ python-version: 3.9
24
 
25
+ - name: Install feeed
26
+ run: |
27
+ python -m pip install --upgrade pip
28
+ pip install .
 
 
29
 
30
  - name: Run test
31
+ run:
 
32
  python main.py -o config_files/options/baseline.json -a config_files/algorithm/pipeline_steps/feature_extraction.json
33
 
34
  - name: Compare output
 
38
  test_generation:
39
  runs-on: ubuntu-latest
40
 
41
+ # Setting up a python envronment for the test script to run
42
  steps:
43
  - name: Checkout code
44
  uses: actions/checkout@v4
45
 
46
+ - name: Set up Python
47
+ uses: actions/setup-python@v5
48
+ with:
49
+ python-version: 3.9
50
 
51
+ - name: Install dependencies
52
+ run: |
53
+ sudo apt-get install build-essential python3 python3-dev
54
 
55
+ - name: Install feeed
56
+ run: |
57
+ python -m pip install --upgrade pip
58
+ pip install .
59
 
60
  - name: Run test
61
+ run:
 
62
  python main.py -o config_files/options/baseline.json -a config_files/algorithm/pipeline_steps/generation.json
63
 
64
  - name: Compare output 1
65
+ run:
66
+ diff data/validation/genELexperiment2_07_04.json output/features/grid_feat/2_enself_rt20v/genELexperiment2_07_04.json
67
 
68
  - name: Compare output 2
69
+ run:
70
+ diff data/validation/genELexperiment1_04_02.json output/features/grid_feat/2_enself_rt20v/genELexperiment1_04_02.json
71
 
72
  - name: Compare output 3
73
+ run:
74
+ diff data/validation/genELexperiment3_04.json output/features/grid_feat/1_enself/genELexperiment3_04.json
75
 
76
  - name: Compare output 4
77
+ run:
78
+ diff data/validation/genELexperiment4_02.json output/features/grid_feat/1_rt20v/genELexperiment4_02.json
79
 
80
  test_benchmark:
81
  runs-on: ubuntu-latest
82
 
83
+ # Setting up a python envronment for the test script to run
84
  steps:
85
  - name: Checkout code
86
  uses: actions/checkout@v4
87
 
88
+ - name: Set up Python
89
+ uses: actions/setup-python@v5
90
+ with:
91
+ python-version: 3.9
92
 
93
+ - name: Install feeed
94
+ run: |
95
+ python -m pip install --upgrade pip
96
+ pip install .
 
 
97
 
98
  - name: Run test
99
+ run:
 
100
  python main.py -o config_files/options/baseline.json -a config_files/algorithm/pipeline_steps/benchmark.json
101
 
102
  - name: Convert output and validation to same encoding
 
109
  test_augmentation:
110
  runs-on: ubuntu-latest
111
 
112
+ # Setting up a python envronment for the test script to run
113
  steps:
114
  - name: Checkout code
115
  uses: actions/checkout@v4
116
 
117
+ - name: Set up Python
118
+ uses: actions/setup-python@v5
119
+ with:
120
+ python-version: 3.9
121
 
122
+ - name: Install feeed
123
+ run: |
124
+ python -m pip install --upgrade pip
125
+ pip install .
 
 
126
 
127
  - name: Run test
128
+ run:
 
129
  python main.py -o config_files/options/baseline.json -a config_files/algorithm/pipeline_steps/augmentation.json
130
 
 
131
  test_evaluation-plotter:
132
  runs-on: ubuntu-latest
133
 
134
+ # Setting up a python envronment for the test script to run
135
  steps:
136
  - name: Checkout code
137
  uses: actions/checkout@v4
138
 
139
+ - name: Set up Python
140
+ uses: actions/setup-python@v5
141
+ with:
142
+ python-version: 3.9
143
 
144
+ - name: Install dependencies
145
+ run: |
146
+ sudo apt-get install build-essential python3 python3-dev
147
 
148
+ - name: Install feeed
149
+ run: |
150
+ python -m pip install --upgrade pip
151
+ pip install .
152
 
153
  - name: Run test
154
+ run:
 
 
155
 
156
+ python main.py -o config_files/options/baseline.json -a config_files/algorithm/pipeline_steps/evaluation_plotter.json
157
 
158
  test_integration:
159
  runs-on: ubuntu-latest
160
 
161
+ # Setting up a python envronment for the test script to run
162
  steps:
163
  - name: Checkout code
164
  uses: actions/checkout@v4
165
 
166
+ - name: Set up Python
167
+ uses: actions/setup-python@v5
168
+ with:
169
+ python-version: 3.9
170
 
171
+ - name: Install dependencies
172
+ run: |
173
+ sudo apt-get install build-essential python3 python3-dev
174
 
175
+ - name: Install feeed
176
+ run: |
177
+ python -m pip install --upgrade pip
178
+ pip install .
179
 
180
  - name: Run test
181
+ run:
 
182
  python main.py -o config_files/options/baseline.json -a config_files/algorithm/experiment_test.json
183
 
 
184
  test_grid_experiments_script:
185
  runs-on: ubuntu-latest
186
 
187
+ # Setting up a python envronment for the test script to run
188
  steps:
189
  - name: Checkout code
190
  uses: actions/checkout@v4
191
 
192
+ - name: Set up Python
193
+ uses: actions/setup-python@v5
194
+ with:
195
+ python-version: 3.9
196
 
197
+ - name: Install dependencies
198
+ run: |
199
+ sudo apt-get install build-essential python3 python3-dev
200
 
201
+ - name: Install feeed
202
+ run: |
203
+ python -m pip install --upgrade pip
204
+ pip install .
205
 
206
  - name: Run test
207
+ run:
 
208
  python execute_grid_experiments.py config_files/algorithm/test
209
 
210
  - name: Convert output and validation to same encoding
211
  run: iconv -f UTF-8 -t ASCII output/features/generated/2_bpic_features/2_ense_enseef_feat.csv > data/validation/2_ense_enseef_feat.csv
212
 
213
  - name: Compare output
214
+ run: diff data/validation/2_ense_enseef_feat.csv output/features/generated/2_bpic_features/2_ense_enseef_feat.csv