From 72936ca34d191151a844dafb9945c12c2972e472 Mon Sep 17 00:00:00 2001
From: SarahAlidoost <f.alidoost@esciencecenter.nl>
Date: Mon, 12 Aug 2024 17:11:47 +0200
Subject: [PATCH 01/22] add a linter workflow for changed files in a PR

---
 .github/workflows/lint.yml | 28 ++++++++++++++++++++++++++++
 1 file changed, 28 insertions(+)
 create mode 100644 .github/workflows/lint.yml

diff --git a/.github/workflows/lint.yml b/.github/workflows/lint.yml
new file mode 100644
index 0000000..80e6b39
--- /dev/null
+++ b/.github/workflows/lint.yml
@@ -0,0 +1,28 @@
+name: Linting
+
+on:
+  pull_request:  # only run on pull requests for now
+    branches: [ "master", "development" ]
+
+jobs:
+  lint:
+      runs-on: ubuntu-latest
+      defaults:
+        run:
+          working-directory: ./dgl_ptm
+      steps:
+        - uses: actions/checkout@v3
+        - name: Set up Python 3.11
+          uses: actions/setup-python@v3
+          with:
+            python-version: "3.11"
+        - name: Install dependencies
+          run: |
+            python -m pip install --upgrade pip
+            python -m pip install .[dev]
+        - name: Get changed files  # for now, we only lint the changed files
+          id: files
+          run: |
+            echo "::set-output name=files::$(git diff --name-only origin/${{ github.base_ref }}...HEAD)"
+        - name: Check code style against standards
+          run: ruff check ${{ steps.files.outputs.files }}
\ No newline at end of file

From c75fcc77438a6d5b3230a3a291cf23186179b093 Mon Sep 17 00:00:00 2001
From: SarahAlidoost <f.alidoost@esciencecenter.nl>
Date: Mon, 12 Aug 2024 17:20:33 +0200
Subject: [PATCH 02/22] lint the files in dgl_ptm and tests dirs

---
 .github/workflows/lint.yml | 16 +++++++++++-----
 1 file changed, 11 insertions(+), 5 deletions(-)

diff --git a/.github/workflows/lint.yml b/.github/workflows/lint.yml
index 80e6b39..6154431 100644
--- a/.github/workflows/lint.yml
+++ b/.github/workflows/lint.yml
@@ -20,9 +20,15 @@ jobs:
           run: |
             python -m pip install --upgrade pip
             python -m pip install .[dev]
-        - name: Get changed files  # for now, we only lint the changed files
-          id: files
+        - name: Get changed files in dgl_ptm folder  # for now, we only lint the changed files
+          id: dgl_ptm
           run: |
-            echo "::set-output name=files::$(git diff --name-only origin/${{ github.base_ref }}...HEAD)"
-        - name: Check code style against standards
-          run: ruff check ${{ steps.files.outputs.files }}
\ No newline at end of file
+            echo "::set-output name=dgl_ptm::$(git diff --name-only origin/${{ github.base_ref }}...HEAD | grep '^dgl_ptm/')"
+        - name: Check source code style against standards
+          run: ruff check ${{ steps.dgl_ptm.outputs.dgl_ptm }}
+        - name: Get changed files in tests folder  # for now, we only lint the changed files
+          id: tests
+          run: |
+            echo "::set-output name=tests::$(git diff --name-only origin/${{ github.base_ref }}...HEAD | grep '^tests/')"
+        - name: Check tests code style against standards
+          run: ruff check ${{ steps.tests.outputs.tests }}
\ No newline at end of file

From d85b89165a74aa93b340ac555787ff4d5863940a Mon Sep 17 00:00:00 2001
From: SarahAlidoost <f.alidoost@esciencecenter.nl>
Date: Mon, 12 Aug 2024 17:46:45 +0200
Subject: [PATCH 03/22] fix base_ref and warning message

---
 .github/workflows/lint.yml | 8 ++++++--
 1 file changed, 6 insertions(+), 2 deletions(-)

diff --git a/.github/workflows/lint.yml b/.github/workflows/lint.yml
index 6154431..ec59608 100644
--- a/.github/workflows/lint.yml
+++ b/.github/workflows/lint.yml
@@ -12,6 +12,8 @@ jobs:
           working-directory: ./dgl_ptm
       steps:
         - uses: actions/checkout@v3
+          with:
+            fetch-depth: 0
         - name: Set up Python 3.11
           uses: actions/setup-python@v3
           with:
@@ -23,12 +25,14 @@ jobs:
         - name: Get changed files in dgl_ptm folder  # for now, we only lint the changed files
           id: dgl_ptm
           run: |
-            echo "::set-output name=dgl_ptm::$(git diff --name-only origin/${{ github.base_ref }}...HEAD | grep '^dgl_ptm/')"
+            git diff --name-only ${{ github.base_ref }}...HEAD | grep '^dgl_ptm/' > $GITHUB_ENV
+            echo "dgl_ptm=$(cat $GITHUB_ENV)" >> $GITHUB_ENV
         - name: Check source code style against standards
           run: ruff check ${{ steps.dgl_ptm.outputs.dgl_ptm }}
         - name: Get changed files in tests folder  # for now, we only lint the changed files
           id: tests
           run: |
-            echo "::set-output name=tests::$(git diff --name-only origin/${{ github.base_ref }}...HEAD | grep '^tests/')"
+            git diff --name-only ${{ github.base_ref }}...HEAD | grep '^dgl_ptm/' > $GITHUB_ENV
+            echo "tests=$(cat $GITHUB_ENV)" >> $GITHUB_ENV
         - name: Check tests code style against standards
           run: ruff check ${{ steps.tests.outputs.tests }}
\ No newline at end of file

From 4a5c64ed76fc880a4314f30ec4ceb921a67106e4 Mon Sep 17 00:00:00 2001
From: SarahAlidoost <f.alidoost@esciencecenter.nl>
Date: Mon, 12 Aug 2024 17:48:37 +0200
Subject: [PATCH 04/22] remove fetch

---
 .github/workflows/lint.yml | 2 --
 1 file changed, 2 deletions(-)

diff --git a/.github/workflows/lint.yml b/.github/workflows/lint.yml
index ec59608..2cc53f3 100644
--- a/.github/workflows/lint.yml
+++ b/.github/workflows/lint.yml
@@ -12,8 +12,6 @@ jobs:
           working-directory: ./dgl_ptm
       steps:
         - uses: actions/checkout@v3
-          with:
-            fetch-depth: 0
         - name: Set up Python 3.11
           uses: actions/setup-python@v3
           with:

From caa8986c599d0fbbdaad47a69f4a90f39095395d Mon Sep 17 00:00:00 2001
From: SarahAlidoost <f.alidoost@esciencecenter.nl>
Date: Thu, 15 Aug 2024 12:13:01 +0200
Subject: [PATCH 05/22] fix linter workflow

---
 .github/workflows/lint.yml | 18 ++++++------------
 1 file changed, 6 insertions(+), 12 deletions(-)

diff --git a/.github/workflows/lint.yml b/.github/workflows/lint.yml
index 2cc53f3..97d1b92 100644
--- a/.github/workflows/lint.yml
+++ b/.github/workflows/lint.yml
@@ -12,6 +12,8 @@ jobs:
           working-directory: ./dgl_ptm
       steps:
         - uses: actions/checkout@v3
+          with:
+            fetch-depth: 0
         - name: Set up Python 3.11
           uses: actions/setup-python@v3
           with:
@@ -20,17 +22,9 @@ jobs:
           run: |
             python -m pip install --upgrade pip
             python -m pip install .[dev]
-        - name: Get changed files in dgl_ptm folder  # for now, we only lint the changed files
-          id: dgl_ptm
+        - name: Get changed files folder  # for now, we only lint the changed files
+          id: files
           run: |
-            git diff --name-only ${{ github.base_ref }}...HEAD | grep '^dgl_ptm/' > $GITHUB_ENV
-            echo "dgl_ptm=$(cat $GITHUB_ENV)" >> $GITHUB_ENV
+            echo "files=$(git diff --name-only --diff-filter=d $GITHUB_BASE_REF...HEAD)" >> $GITHUB_ENV
         - name: Check source code style against standards
-          run: ruff check ${{ steps.dgl_ptm.outputs.dgl_ptm }}
-        - name: Get changed files in tests folder  # for now, we only lint the changed files
-          id: tests
-          run: |
-            git diff --name-only ${{ github.base_ref }}...HEAD | grep '^dgl_ptm/' > $GITHUB_ENV
-            echo "tests=$(cat $GITHUB_ENV)" >> $GITHUB_ENV
-        - name: Check tests code style against standards
-          run: ruff check ${{ steps.tests.outputs.tests }}
\ No newline at end of file
+          run: ruff check $(echo ${{ env.files }} | tr ' ' '\n')

From 62bb9f894db9c9aa65d52756422b86cdd564389b Mon Sep 17 00:00:00 2001
From: SarahAlidoost <f.alidoost@esciencecenter.nl>
Date: Thu, 15 Aug 2024 13:40:06 +0200
Subject: [PATCH 06/22] fix diff command

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

diff --git a/.github/workflows/lint.yml b/.github/workflows/lint.yml
index 97d1b92..8073ddc 100644
--- a/.github/workflows/lint.yml
+++ b/.github/workflows/lint.yml
@@ -25,6 +25,6 @@ jobs:
         - name: Get changed files folder  # for now, we only lint the changed files
           id: files
           run: |
-            echo "files=$(git diff --name-only --diff-filter=d $GITHUB_BASE_REF...HEAD)" >> $GITHUB_ENV
+            echo "files=$(git diff --name-only --diff-filter=d origin/$GITHUB_BASE_REF...origin/$GITHUB_HEAD_REF)" >> $GITHUB_ENV
         - name: Check source code style against standards
           run: ruff check $(echo ${{ env.files }} | tr ' ' '\n')

From 53ecf2b1f2d08d764ae9e68d8d9b54853fca523d Mon Sep 17 00:00:00 2001
From: SarahAlidoost <f.alidoost@esciencecenter.nl>
Date: Thu, 15 Aug 2024 14:10:54 +0200
Subject: [PATCH 07/22] set working dir for git diff

---
 .github/workflows/lint.yml | 4 ++--
 1 file changed, 2 insertions(+), 2 deletions(-)

diff --git a/.github/workflows/lint.yml b/.github/workflows/lint.yml
index 8073ddc..ddd7114 100644
--- a/.github/workflows/lint.yml
+++ b/.github/workflows/lint.yml
@@ -22,9 +22,9 @@ jobs:
           run: |
             python -m pip install --upgrade pip
             python -m pip install .[dev]
-        - name: Get changed files folder  # for now, we only lint the changed files
+        - name: Get changed files in dgl_ptm # for now, we only lint the changed files
           id: files
           run: |
-            echo "files=$(git diff --name-only --diff-filter=d origin/$GITHUB_BASE_REF...origin/$GITHUB_HEAD_REF)" >> $GITHUB_ENV
+            echo "files=$(git diff --name-only --diff-filter=d origin/$GITHUB_BASE_REF...origin/$GITHUB_HEAD_REF -- ./dgl_ptm)" >> $GITHUB_ENV
         - name: Check source code style against standards
           run: ruff check $(echo ${{ env.files }} | tr ' ' '\n')

From 4471511e082603adc745ae2a305bc5e49f22712d Mon Sep 17 00:00:00 2001
From: SarahAlidoost <f.alidoost@esciencecenter.nl>
Date: Thu, 15 Aug 2024 14:38:00 +0200
Subject: [PATCH 08/22] ruff check only if files are changed in dgl_ptm dir

---
 .github/workflows/lint.yml | 12 ++++++------
 1 file changed, 6 insertions(+), 6 deletions(-)

diff --git a/.github/workflows/lint.yml b/.github/workflows/lint.yml
index ddd7114..1df64e8 100644
--- a/.github/workflows/lint.yml
+++ b/.github/workflows/lint.yml
@@ -18,13 +18,13 @@ jobs:
           uses: actions/setup-python@v3
           with:
             python-version: "3.11"
-        - name: Install dependencies
-          run: |
-            python -m pip install --upgrade pip
-            python -m pip install .[dev]
         - name: Get changed files in dgl_ptm # for now, we only lint the changed files
           id: files
           run: |
             echo "files=$(git diff --name-only --diff-filter=d origin/$GITHUB_BASE_REF...origin/$GITHUB_HEAD_REF -- ./dgl_ptm)" >> $GITHUB_ENV
-        - name: Check source code style against standards
-          run: ruff check $(echo ${{ env.files }} | tr ' ' '\n')
+        - name: Check code style against standards
+          if: env.files != ''
+          run: |
+            python -m pip install --upgrade pip
+            python -m pip install .[dev]
+            ruff check $(echo ${{ env.files }} | tr ' ' '\n')

From 317f1bf5492c7ecacfc845b077dd1c2d02e313b3 Mon Sep 17 00:00:00 2001
From: SarahAlidoost <f.alidoost@esciencecenter.nl>
Date: Thu, 15 Aug 2024 14:46:48 +0200
Subject: [PATCH 09/22] fix linter errors on test_config

---
 dgl_ptm/tests/test_config.py | 3 ++-
 1 file changed, 2 insertions(+), 1 deletion(-)

diff --git a/dgl_ptm/tests/test_config.py b/dgl_ptm/tests/test_config.py
index 5799fb6..073e40b 100644
--- a/dgl_ptm/tests/test_config.py
+++ b/dgl_ptm/tests/test_config.py
@@ -4,6 +4,7 @@
 
 from dgl_ptm.config import Config
 
+
 @pytest.fixture
 def config_parameters():
     return {
@@ -43,7 +44,7 @@ def test_to_yaml(tmp_path):
     cfg = Config()
     cfg.to_yaml(tmp_path / "config.yaml")
 
-    with open(tmp_path / "config.yaml", "r") as f:
+    with open(tmp_path / "config.yaml") as f:
         cfg_dict = yaml.safe_load(f)
     assert cfg_dict["_model_identifier"] == "test"
     assert cfg_dict["number_agents"] == 100

From 5cfb6a4746cf68eb88e9d1be5f49055124625e1e Mon Sep 17 00:00:00 2001
From: SarahAlidoost <f.alidoost@esciencecenter.nl>
Date: Thu, 15 Aug 2024 15:47:21 +0200
Subject: [PATCH 10/22] add a debug step

---
 .github/workflows/lint.yml | 3 +++
 1 file changed, 3 insertions(+)

diff --git a/.github/workflows/lint.yml b/.github/workflows/lint.yml
index 1df64e8..63b7743 100644
--- a/.github/workflows/lint.yml
+++ b/.github/workflows/lint.yml
@@ -28,3 +28,6 @@ jobs:
             python -m pip install --upgrade pip
             python -m pip install .[dev]
             ruff check $(echo ${{ env.files }} | tr ' ' '\n')
+        - name: Print message when files is empty
+          if: env.files == ''
+          run: echo "No files were changed."

From 0623d9873dbbc2d8f23eb8e3eacedcc939ed397e Mon Sep 17 00:00:00 2001
From: SarahAlidoost <f.alidoost@esciencecenter.nl>
Date: Thu, 15 Aug 2024 15:51:57 +0200
Subject: [PATCH 11/22] a minor edit to test_config

---
 dgl_ptm/tests/test_config.py | 2 +-
 1 file changed, 1 insertion(+), 1 deletion(-)

diff --git a/dgl_ptm/tests/test_config.py b/dgl_ptm/tests/test_config.py
index 073e40b..d4b6d74 100644
--- a/dgl_ptm/tests/test_config.py
+++ b/dgl_ptm/tests/test_config.py
@@ -59,7 +59,7 @@ def test_invalid_fields(config_parameters):
         _ = Config.from_dict(config_parameters)
 
 def test_invalid_values(config_parameters):
-    """Test that invalid values are not accepted."""
+    """Test invalid values."""
     config_parameters["number_agents"] = -100
     with pytest.raises(ValueError):
         _ = Config.from_dict(config_parameters)

From ddb01cda8213bcea4b1049855060df17412a2ef9 Mon Sep 17 00:00:00 2001
From: SarahAlidoost <f.alidoost@esciencecenter.nl>
Date: Thu, 15 Aug 2024 16:00:19 +0200
Subject: [PATCH 12/22] fix email address in init

---
 dgl_ptm/dgl_ptm/__init__.py | 2 +-
 1 file changed, 1 insertion(+), 1 deletion(-)

diff --git a/dgl_ptm/dgl_ptm/__init__.py b/dgl_ptm/dgl_ptm/__init__.py
index d629b89..a21976b 100644
--- a/dgl_ptm/dgl_ptm/__init__.py
+++ b/dgl_ptm/dgl_ptm/__init__.py
@@ -13,5 +13,5 @@
 logging.getLogger(__name__).addHandler(logging.NullHandler())
 
 __author__ = "Team Atlas"
-__email__ = "p.chandramouli@esciencecenter.nl"
+__email__ = "m.grootes@esciencecenter.nl"
 __version__ = "0.1.0"

From 31ec4f43cdf40d4a119450e1c7a8f628e4a7caa1 Mon Sep 17 00:00:00 2001
From: SarahAlidoost <f.alidoost@esciencecenter.nl>
Date: Thu, 15 Aug 2024 16:23:00 +0200
Subject: [PATCH 13/22] remove install dependencies

---
 .github/workflows/lint.yml | 9 +++------
 1 file changed, 3 insertions(+), 6 deletions(-)

diff --git a/.github/workflows/lint.yml b/.github/workflows/lint.yml
index 63b7743..dd4fe53 100644
--- a/.github/workflows/lint.yml
+++ b/.github/workflows/lint.yml
@@ -7,9 +7,6 @@ on:
 jobs:
   lint:
       runs-on: ubuntu-latest
-      defaults:
-        run:
-          working-directory: ./dgl_ptm
       steps:
         - uses: actions/checkout@v3
           with:
@@ -18,15 +15,15 @@ jobs:
           uses: actions/setup-python@v3
           with:
             python-version: "3.11"
-        - name: Get changed files in dgl_ptm # for now, we only lint the changed files
+        - name: Get changed python files # for now, we only lint the changed files
           id: files
           run: |
-            echo "files=$(git diff --name-only --diff-filter=d origin/$GITHUB_BASE_REF...origin/$GITHUB_HEAD_REF -- ./dgl_ptm)" >> $GITHUB_ENV
+            echo "files=$(git diff --name-only --diff-filter=d origin/$GITHUB_BASE_REF...origin/$GITHUB_HEAD_REF -- '*.py')" >> $GITHUB_ENV
         - name: Check code style against standards
           if: env.files != ''
           run: |
             python -m pip install --upgrade pip
-            python -m pip install .[dev]
+            python -m pip install ruff
             ruff check $(echo ${{ env.files }} | tr ' ' '\n')
         - name: Print message when files is empty
           if: env.files == ''

From b164bac314944c53e37cf862a795d2dece062784 Mon Sep 17 00:00:00 2001
From: SarahAlidoost <f.alidoost@esciencecenter.nl>
Date: Thu, 15 Aug 2024 16:48:05 +0200
Subject: [PATCH 14/22] bring back install dependencies, set relative for git
 diff

---
 .github/workflows/lint.yml | 10 +++++++---
 1 file changed, 7 insertions(+), 3 deletions(-)

diff --git a/.github/workflows/lint.yml b/.github/workflows/lint.yml
index dd4fe53..7e3eac6 100644
--- a/.github/workflows/lint.yml
+++ b/.github/workflows/lint.yml
@@ -7,6 +7,9 @@ on:
 jobs:
   lint:
       runs-on: ubuntu-latest
+      defaults:
+        run:
+          working-directory: ./dgl_ptm
       steps:
         - uses: actions/checkout@v3
           with:
@@ -15,15 +18,16 @@ jobs:
           uses: actions/setup-python@v3
           with:
             python-version: "3.11"
-        - name: Get changed python files # for now, we only lint the changed files
+        - name: Get changed files in dgl_ptm # for now, we only lint the changed files
           id: files
           run: |
-            echo "files=$(git diff --name-only --diff-filter=d origin/$GITHUB_BASE_REF...origin/$GITHUB_HEAD_REF -- '*.py')" >> $GITHUB_ENV
+            echo "files=$(git diff --name-only --relative --diff-filter=d origin/$GITHUB_BASE_REF...origin/$GITHUB_HEAD_REF)" >> $GITHUB_ENV
+            echo ${{ env.files }}
         - name: Check code style against standards
           if: env.files != ''
           run: |
             python -m pip install --upgrade pip
-            python -m pip install ruff
+            python -m pip install .[dev]
             ruff check $(echo ${{ env.files }} | tr ' ' '\n')
         - name: Print message when files is empty
           if: env.files == ''

From 46938ed163b30a9364cecead4a6ed5faa28db3cd Mon Sep 17 00:00:00 2001
From: SarahAlidoost <f.alidoost@esciencecenter.nl>
Date: Thu, 15 Aug 2024 17:12:39 +0200
Subject: [PATCH 15/22] fix the format of env

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

diff --git a/.github/workflows/lint.yml b/.github/workflows/lint.yml
index 7e3eac6..1542af7 100644
--- a/.github/workflows/lint.yml
+++ b/.github/workflows/lint.yml
@@ -21,7 +21,7 @@ jobs:
         - name: Get changed files in dgl_ptm # for now, we only lint the changed files
           id: files
           run: |
-            echo "files=$(git diff --name-only --relative --diff-filter=d origin/$GITHUB_BASE_REF...origin/$GITHUB_HEAD_REF)" >> $GITHUB_ENV
+            echo "files=$(git diff --name-only --relative --diff-filter=d origin/$GITHUB_BASE_REF...origin/$GITHUB_HEAD_REF | tr '\n' ' ')" >> $GITHUB_ENV
             echo ${{ env.files }}
         - name: Check code style against standards
           if: env.files != ''

From 1f9e1a241c8237082be923332ad88e5078992141 Mon Sep 17 00:00:00 2001
From: SarahAlidoost <f.alidoost@esciencecenter.nl>
Date: Thu, 15 Aug 2024 17:24:40 +0200
Subject: [PATCH 16/22] fix linter errors of init

---
 dgl_ptm/dgl_ptm/__init__.py | 9 ++++++---
 1 file changed, 6 insertions(+), 3 deletions(-)

diff --git a/dgl_ptm/dgl_ptm/__init__.py b/dgl_ptm/dgl_ptm/__init__.py
index a21976b..7bd8b0d 100644
--- a/dgl_ptm/dgl_ptm/__init__.py
+++ b/dgl_ptm/dgl_ptm/__init__.py
@@ -1,8 +1,6 @@
-"""Documentation about dgl_ptm"""
+"""Documentation about dgl_ptm."""
 import logging
 
-#from dgl_ptm.model import initialize_model, step
-from dgl_ptm.model.initialize_model import PovertyTrapModel
 # from dgl_ptm.agent import agent_update
 # from dgl_ptm.agentInteraction import trade_money
 # from dgl_ptm.network import global_attachment, link_deletion
@@ -10,6 +8,11 @@
 # from dgl_ptm.util import *
 from dgl_ptm import config
 
+#from dgl_ptm.model import initialize_model, step
+from dgl_ptm.model.initialize_model import PovertyTrapModel
+
+__all__ = ['config', 'PovertyTrapModel']
+
 logging.getLogger(__name__).addHandler(logging.NullHandler())
 
 __author__ = "Team Atlas"

From 80bd7375192488b32f5dd9731a08339bfca30afa Mon Sep 17 00:00:00 2001
From: SarahAlidoost <f.alidoost@esciencecenter.nl>
Date: Thu, 15 Aug 2024 17:25:35 +0200
Subject: [PATCH 17/22] remove debuging from the lint workflow

---
 .github/workflows/lint.yml | 6 ++++--
 1 file changed, 4 insertions(+), 2 deletions(-)

diff --git a/.github/workflows/lint.yml b/.github/workflows/lint.yml
index 1542af7..b3ab554 100644
--- a/.github/workflows/lint.yml
+++ b/.github/workflows/lint.yml
@@ -22,12 +22,14 @@ jobs:
           id: files
           run: |
             echo "files=$(git diff --name-only --relative --diff-filter=d origin/$GITHUB_BASE_REF...origin/$GITHUB_HEAD_REF | tr '\n' ' ')" >> $GITHUB_ENV
-            echo ${{ env.files }}
-        - name: Check code style against standards
+        - name:  Install dependencies  # ruff tools are installed in the dev dependencies
           if: env.files != ''
           run: |
             python -m pip install --upgrade pip
             python -m pip install .[dev]
+        - name: Check code style against standards
+          if: env.files != ''
+          run: |
             ruff check $(echo ${{ env.files }} | tr ' ' '\n')
         - name: Print message when files is empty
           if: env.files == ''

From 0fbb8c28b3febebe3af7f4b31d4127c9d0d203ed Mon Sep 17 00:00:00 2001
From: Victoria <victoria@wcw-staff-145-109-80-121.wireless.uva.nl>
Date: Fri, 16 Aug 2024 13:48:50 +0200
Subject: [PATCH 18/22] minor cleaning of unused comments and print statements

---
 dgl_ptm/dgl_ptm/agent/wealth_consumption.py | 10 ++---
 dgl_ptm/dgl_ptm/model/initialize_model.py   | 42 ---------------------
 2 files changed, 3 insertions(+), 49 deletions(-)

diff --git a/dgl_ptm/dgl_ptm/agent/wealth_consumption.py b/dgl_ptm/dgl_ptm/agent/wealth_consumption.py
index 094cc84..287dec8 100644
--- a/dgl_ptm/dgl_ptm/agent/wealth_consumption.py
+++ b/dgl_ptm/dgl_ptm/agent/wealth_consumption.py
@@ -188,7 +188,7 @@ def  _nn_bellman_past_shock_consumption(model_graph,model_params, timestep, devi
     if model_params['nn_path']==None:
         print("No consumption model path provided!")
     
-    #load model  
+    # Load model  
     
     estimator,scale = load_consumption_model(model_params['nn_path'],device)  
 
@@ -197,21 +197,17 @@ def  _nn_bellman_past_shock_consumption(model_graph,model_params, timestep, devi
 
     input = torch.cat((model_graph.ndata['alpha'].unsqueeze(1), model_graph.ndata['wealth'].unsqueeze(1), model_graph.ndata['sigma'].unsqueeze(1), model_graph.ndata['theta'].unsqueeze(1)), dim=1) 
     
-    #forward pass to get predictions
+    # Forward pass to get predictions
     with torch.no_grad():
 
         pred=estimator(input)
-
-    #print(" went forward, writing values")
-
     
     model_graph.ndata['m'],model_graph.ndata['i_a']=model_graph.ndata['a_table'][torch.arange(model_graph.ndata['a_table'].size(0)),:,torch.argmin(torch.abs(pred[:, 0].unsqueeze(1) - model_graph.ndata['a_table'][:,1,:]), dim=1)].unbind(dim=1)
     
     #print("Cleaning output and checking for violations")
 
-    #Clean Consumption
+    # Clean Consumption
     model_graph.ndata['wealth_consumption']=(pred[:,1]*scale).clamp_(min=0)
-    #print(" violation check")
 
     # Check for violations
     # An equation violation occurs when personally shocked, depreciated k + income - consumption - i_a is less than or equal to 0
diff --git a/dgl_ptm/dgl_ptm/model/initialize_model.py b/dgl_ptm/dgl_ptm/model/initialize_model.py
index 4ada728..cde91ff 100644
--- a/dgl_ptm/dgl_ptm/model/initialize_model.py
+++ b/dgl_ptm/dgl_ptm/model/initialize_model.py
@@ -90,48 +90,6 @@ class PovertyTrapModel(Model):
     """
     Poverty Trap model as derived model class
 
-    default_model_parameters = {'number_agents': 100 , 
-    'seed':0,
-    'gamma_vals':torch.tensor([0.3,0.45]) , #for pseudo income
-    'sigma_dist': {'type':'uniform','parameters':[0.05,1.94],'round':True,'decimals':1},
-    'cost_vals': torch.tensor([0.,0.45]), #for pseudo income
-    'tec_levels': torch.tensor([0,1]), #check if deletable
-    'a_theta_dist': {'type':'uniform','parameters':[0.1,1],'round':False,'decimals':None},
-    'sensitivity_dist':{'type':'uniform','parameters':[0.0,1],'round':False,'decimals':None},
-    'tec_dist': {'type':'bernoulli','parameters':[0.5,None],'round':False,'decimals':None},
-    'capital_dist': {'type':'uniform','parameters':[0.1,10.],'round':False,'decimals':None},
-    'alpha_dist': {'type':'normal','parameters':[1.08,0.074],'round':False,'decimals':None},
-    'lam_dist': {'type':'uniform','parameters':[0.05,0.94],'round':True,'decimals':1},
-    'initial_graph_type': 'barabasi-albert',
-    'initial_graph_args': {'seed': 0, 'new_node_edges':1},
-    'device': 'cpu',
-    'step_count':0,
-    'step_target':20,
-    'steering_parameters':{'npath':'./agent_data.zarr',
-                            'epath':'./edge_data',
-                            'ndata':['all_except',['a_table']],
-                            'edata':['all'],
-                            'mode':'xarray',
-                            'wealth_method':'singular_transfer',
-                            'income_method':'pseudo_income_generation',
-                            'tech_gamma': torch.tensor([0.3,0.35,0.45]),
-                            'tech_cost': torch.tensor([0,0.15,0.65]),
-                            'consume_method':'pseudo_consumption',
-                            'nn_path': None,
-                            'adapt_m':torch.tensor([0,0.5,0.9]),
-                            'adapt_cost':torch.tensor([0,0.25,0.45]),
-                            'depreciation': 0.6,
-                            'discount': 0.95,
-                            'm_theta_dist': {'type':'multinomial','parameters':[[0.02 ,0.03, 0.05, 0.9],[0.7, 0.8, 0.9, 1]],'round':False,'decimals':None},
-                            'm_attach_dist': {'type':'uniform','parameters':[0.001,1],'round':False,'decimals':None},
-                            'del_method':'probability',
-                            'del_threshold':0.05,
-                            'ratio':0.1,
-                            'weight_a':0.69,
-                            'weight_b':35,
-                            'truncation_weight':1.0e-10,
-                            'step_type':'default'}}
-
     """
 
     def __init__(self,*, model_identifier):

From 533f350ffb24c4af9cc19b12ba27e72bee2f2394 Mon Sep 17 00:00:00 2001
From: SarahAlidoost <f.alidoost@esciencecenter.nl>
Date: Mon, 19 Aug 2024 14:38:17 +0200
Subject: [PATCH 19/22] set some linter parameters in pyproject.toml

---
 dgl_ptm/pyproject.toml | 24 +++++++++++++++++++-----
 1 file changed, 19 insertions(+), 5 deletions(-)

diff --git a/dgl_ptm/pyproject.toml b/dgl_ptm/pyproject.toml
index 48a7322..a833142 100644
--- a/dgl_ptm/pyproject.toml
+++ b/dgl_ptm/pyproject.toml
@@ -36,8 +36,6 @@ classifiers=[
     'Intended Audience :: Developers',
     'License :: OSI Approved :: Apache Software License',
     'Natural Language :: English',
-    'Programming Language :: Python :: 3.9',
-    'Programming Language :: Python :: 3.10',
     'Programming Language :: Python :: 3.11',
 ]
 
@@ -89,16 +87,32 @@ select = [
   "N",  # PEP8-naming
   "UP",  # pyupgrade (upgrade syntax to current syntax)
   "PLE",  # Pylint error https://github.com/charliermarsh/ruff#error-ple
+  "PLR",  # Pylint refactor (e.g. too-many-arguments)
+  "PLW",  # Pylint warning (useless-else-on-loop)
+]
+extend-select = [
+  "D401",  # First line should be in imperative mood
+  "D400",  # First line should end in a period.
+  "TID252",  # No relative imports (not pep8 compliant)
 ]
 ignore = [
-"D100", "D101", "D104", "D105", "D106", "D107", "D203", "D213"
-] # docstring style
+  "PLR2004",  # magic value used in comparsion.
+  "PLR0913",  # too many arguments
+]
 
 line-length = 88
+
 exclude = ["docs", "build"]
+
 # Allow unused variables when underscore-prefixed.
 dummy-variable-rgx = "^(_+|(_+[a-zA-Z0-9_]*[a-zA-Z0-9]+?))$"
-target-version = "py39"
+target-version = "py311"
 
 [tool.ruff.per-file-ignores]
 "tests/**" = ["D"]
+
+[tool.ruff.lint.pydocstyle]
+convention = "google"
+
+[tool.ruff.lint.mccabe]
+max-complexity = 10

From 97b2ba3c7d41ba93ded79819d11bbfd262f2d67f Mon Sep 17 00:00:00 2001
From: SarahAlidoost <f.alidoost@esciencecenter.nl>
Date: Mon, 19 Aug 2024 14:39:00 +0200
Subject: [PATCH 20/22] lint only python files, add a comment about
 pyproject.toml and ruff settings

---
 .github/workflows/lint.yml | 8 ++++----
 1 file changed, 4 insertions(+), 4 deletions(-)

diff --git a/.github/workflows/lint.yml b/.github/workflows/lint.yml
index b3ab554..9d4eb83 100644
--- a/.github/workflows/lint.yml
+++ b/.github/workflows/lint.yml
@@ -1,4 +1,4 @@
-name: Linting
+name: Linting with ruff  # settings are in pyproject.toml
 
 on:
   pull_request:  # only run on pull requests for now
@@ -18,10 +18,10 @@ jobs:
           uses: actions/setup-python@v3
           with:
             python-version: "3.11"
-        - name: Get changed files in dgl_ptm # for now, we only lint the changed files
+        - name: Get changed python files in dgl_ptm # for now, we only lint the changed files
           id: files
           run: |
-            echo "files=$(git diff --name-only --relative --diff-filter=d origin/$GITHUB_BASE_REF...origin/$GITHUB_HEAD_REF | tr '\n' ' ')" >> $GITHUB_ENV
+            echo "files=$(git diff --name-only --relative --diff-filter=d "*.py" origin/$GITHUB_BASE_REF...origin/$GITHUB_HEAD_REF | tr '\n' ' ')" >> $GITHUB_ENV
         - name:  Install dependencies  # ruff tools are installed in the dev dependencies
           if: env.files != ''
           run: |
@@ -33,4 +33,4 @@ jobs:
             ruff check $(echo ${{ env.files }} | tr ' ' '\n')
         - name: Print message when files is empty
           if: env.files == ''
-          run: echo "No files were changed."
+          run: echo "No python files were changed."

From 7cd8443d40f6b1f0ed4d93f6a631be34f4d2feb1 Mon Sep 17 00:00:00 2001
From: SarahAlidoost <f.alidoost@esciencecenter.nl>
Date: Mon, 19 Aug 2024 15:07:03 +0200
Subject: [PATCH 21/22] fix git diff command in lint workflow

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

diff --git a/.github/workflows/lint.yml b/.github/workflows/lint.yml
index 9d4eb83..ba72927 100644
--- a/.github/workflows/lint.yml
+++ b/.github/workflows/lint.yml
@@ -21,7 +21,7 @@ jobs:
         - name: Get changed python files in dgl_ptm # for now, we only lint the changed files
           id: files
           run: |
-            echo "files=$(git diff --name-only --relative --diff-filter=d "*.py" origin/$GITHUB_BASE_REF...origin/$GITHUB_HEAD_REF | tr '\n' ' ')" >> $GITHUB_ENV
+            echo "files=$(git diff --name-only --relative --diff-filter=d -- "*.py" origin/$GITHUB_BASE_REF...origin/$GITHUB_HEAD_REF | tr '\n' ' ')" >> $GITHUB_ENV
         - name:  Install dependencies  # ruff tools are installed in the dev dependencies
           if: env.files != ''
           run: |

From 6b7e6d45b27d1c61b8a5dfb6f8c6a15a28f632c7 Mon Sep 17 00:00:00 2001
From: SarahAlidoost <f.alidoost@esciencecenter.nl>
Date: Mon, 19 Aug 2024 15:25:32 +0200
Subject: [PATCH 22/22] fix git diff command

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

diff --git a/.github/workflows/lint.yml b/.github/workflows/lint.yml
index ba72927..73ba4bb 100644
--- a/.github/workflows/lint.yml
+++ b/.github/workflows/lint.yml
@@ -21,7 +21,7 @@ jobs:
         - name: Get changed python files in dgl_ptm # for now, we only lint the changed files
           id: files
           run: |
-            echo "files=$(git diff --name-only --relative --diff-filter=d -- "*.py" origin/$GITHUB_BASE_REF...origin/$GITHUB_HEAD_REF | tr '\n' ' ')" >> $GITHUB_ENV
+            echo "files=$(git diff --name-only --relative --diff-filter=d origin/$GITHUB_BASE_REF...origin/$GITHUB_HEAD_REF -- "*.py" | tr '\n' ' ')" >> $GITHUB_ENV
         - name:  Install dependencies  # ruff tools are installed in the dev dependencies
           if: env.files != ''
           run: |