[WIP] Resolve conflicts, add changes back

.github/workflows/codecov.yml

@@ -0,0 +1,50 @@
+name: Code coverage
+
+on: [push, pull_request]
+
+jobs:
+  build:
+    name: Report coverage
+    runs-on: ubuntu-latest
+
+    steps:
+    - uses: actions/checkout@v4
+    - uses: conda-incubator/setup-miniconda@v3
+      with:
+        python-version: 3.11
+        mamba-version: "*"
+        miniforge-version: "latest"
+        channels: conda-forge,defaults
+        channel-priority: true
+        activate-environment: anaconda-client-env
+    - shell: bash -el {0}
+      name: Install dependencies
+      run: |
+        mamba install -y nbmake pytest-xdist line_profiler  # add'l packages for notebook tests.
+        mamba install --file requirements.txt --file requirements-extra.txt
+        python -m pip install -e .
+    - shell: bash -el {0}
+      name: Test with pytest and collect coverage
+      run: |
+        pytest --cov=./ --cov-report=xml
+    - name: Upload coverage to Codecov
+      uses: codecov/codecov-action@v3
+      env:
+        CODECOV_TOKEN: ${{ secrets.CODECOV_TOKEN }}
+
+    - name: Check secret presence
+      id: check_secret
+      run: |
+        echo "is_set=false" >> $GITHUB_OUTPUT
+        if [ ! -z "${{ secrets.CODACY_PROJECT_TOKEN }}" ]; then
+          echo "is_set=true" >> $GITHUB_OUTPUT
+        fi
+
+    - name: Upload coverage to Codacy
+      if: steps.check_secret.outputs.is_set == 'true'
+      uses: codacy/[email protected]
+      with:
+        project-token: ${{ secrets.CODACY_PROJECT_TOKEN }}
+        coverage-reports: coverage.xml
+      env:
+        CODACY_PROJECT_TOKEN: ${{ secrets.CODACY_PROJECT_TOKEN }}

.github/workflows/pythonapp.yml

@@ -38,19 +38,6 @@ jobs:
       name: Test notebooks.
       run: |
         pytest --nbmake examples --ignore=examples/demonstration
-    - shell: bash -el {0}
-      name: Test with pytest and collect coverage
-      run: |
-        pytest --cov=./ --cov-report=xml
-    - name: Upload coverage to Codecov
-      uses: codecov/codecov-action@v3
-      env:
-        CODECOV_TOKEN: ${{ secrets.CODECOV_TOKEN }}
-    - name: Upload coverage to Codacy
-      run: |
-        bash <(curl -Ls https://coverage.codacy.com/get.sh) report -r coverage.xml
-      env:
-        CODACY_PROJECT_TOKEN: ${{ secrets.CODACY_PROJECT_TOKEN }}
     - name: Build a distribution if tagged
       if: github.event_name == 'push' && startsWith(github.ref, 'refs/tags') && matrix.os == 'ubuntu-latest' && matrix.python-version == '3.9'
       run: |
@@ -60,4 +47,4 @@ jobs:
       uses: pypa/gh-action-pypi-publish@release/v1
       with:
         user: __token__
-        password: ${{ secrets.PYPI_PASSWORD }}
+        password: ${{ secrets.PYPI_PASSWORD }}

.gitignore

@@ -38,4 +38,8 @@ icebar
 ~$*.xlsx
 
 # conda
-.conda/*
+.conda/*
+
+# coverage
+.coverage
+coverage.xml

ams/interop/andes.py

@@ -96,9 +96,9 @@ def to_andes(system, setup=False, addfile=None,
     --------
     >>> import ams
     >>> import andes
-    >>> sp = ams.load(ams.get_case('ieee14/ieee14_rted.xlsx'), setup=True)
+    >>> sp = ams.load(ams.get_case('ieee14/ieee14_uced.xlsx'), setup=True)
     >>> sa = sp.to_andes(setup=False,
-    ...                  addfile=andes.get_case('ieee14/ieee14_wt3.xlsx'),
+    ...                  addfile=andes.get_case('ieee14/ieee14_full.xlsx'),
     ...                  overwrite=True, no_output=True)
 
     Notes
@@ -279,9 +279,10 @@ def parse_addfile(adsys, amsys, addfile):
     # add dynamic models
     for name, df in df_models.items():
         # drop rows that all nan
+        df.replace(['', ' '], np.NaN, inplace=True)  # replace empty string with nan
         df.dropna(axis=0, how='all', inplace=True)
         # if the dynamic model also exists in AMS, use AMS parameters for overlap
-        if name in amsys.models.keys():
+        if (name in amsys.models.keys()) and amsys.models[name].n > 0:
             if df.shape[0] != amsys.models[name].n:
                 msg = f'<{name}> has different number of rows in addfile.'
                 logger.warning(msg)
@@ -903,7 +904,6 @@ def make_link_table(adsys):
     ssa_key0 = pd.merge(left=ssa_key0, how='left', on='stg_idx',
                         right=ssa_rg[['stg_idx', 'rg_idx']])
 
-    pd.set_option('future.no_silent_downcasting', True)
     ssa_key0 = ssa_key0.fillna(value=False)
     dyr = ssa_key0['syg_idx'].astype(bool) + ssa_key0['dg_idx'].astype(bool) + ssa_key0['rg_idx'].astype(bool)
     non_dyr = np.logical_not(dyr)
@@ -932,4 +932,4 @@ def make_link_table(adsys):
             'gammap', 'gammaq',                 # gamma
             ]
     out = ssa_key[cols].sort_values(by='stg_idx', ascending=False).reset_index(drop=True)
-    return out
+    return out

ams/routines/routine.py

@@ -693,9 +693,14 @@ def _post_add_check(self):
         """
         Post-addition check.
         """
+        # --- reset routine status ---
         self.initialized = False
         self.exec_time = 0.0
         self.exit_code = 0
+        # --- reset symprocessor status ---
+        self._syms = False
+        # --- reset optimization model status ---
+        self.om.initialized = False
 
     def addRParam(self,
                   name: str,
@@ -786,8 +791,9 @@ def addService(self,
         model : str, optional
             Model name.
         """
-        item = ValueService(name=name, value=value, tex_name=tex_name, unit=unit,
-                            info=info, vtype=vtype, model=model)
+        item = ValueService(name=name, tex_name=tex_name,
+                            unit=unit, info=info,
+                            vtype=vtype, value=value)
         # add the service as an routine attribute
         setattr(self, name, item)
 
@@ -1159,4 +1165,4 @@ def igraph(
             default_name += f"\n${input.tex_name}$" + f" [${input.unit}$]"
         ax.set_title(title if title else default_name, loc=title_loc)
         ig.plot(g, autocurve=autocurve, target=ax, **vstyle)
-        return ax, g
+        return ax, g

docs/source/examples/index.rst

@@ -23,3 +23,4 @@ folder of the repository
    ../_examples/ex5.ipynb
    ../_examples/ex6.ipynb
    ../_examples/ex7.ipynb
+   ../_examples/ex8.ipynb

docs/source/getting_started/formats/xlsx.rst

@@ -13,4 +13,4 @@ Format definition
 The AMS xlsx format contains multiple workbooks (also known as "sheets") shown
 as tabs at the bottom. The name of a workbook is a *model* name, and each
 workbook contains the parameters of all *devices* that are *instances* of the
-model.
+model.

docs/source/index.rst

@@ -106,4 +106,4 @@ dynamic simulator ANDES.
    release-notes
    routineref
    modelref
-   api
+   api

examples/ex1.ipynb

@@ -51,8 +51,8 @@
      "name": "stdout",
      "output_type": "stream",
      "text": [
-      "Last run time: 2024-01-24 09:37:17\n",
-      "ams:0.8.1.post5+ge752692\n"
+      "Last run time: 2024-02-24 17:28:40\n",
+      "ams:0.8.5.post62.dev0+gf6ed683\n"
      ]
     }
    ],
@@ -127,7 +127,7 @@
      "output_type": "stream",
      "text": [
       "Parsing input file \"/Users/jinningwang/Documents/work/ams/ams/cases/5bus/pjm5bus_uced.xlsx\"...\n",
-      "Input file parsed in 0.1218 seconds.\n",
+      "Input file parsed in 0.2701 seconds.\n",
       "Zero line rates detacted in rate_a, rate_b, rate_c, adjusted to 999.\n",
       "If expect a line outage, please set 'u' to 0.\n",
       "System set up in 0.0021 seconds.\n"
@@ -164,33 +164,33 @@
     {
      "data": {
       "text/plain": [
-       "OrderedDict([('Summary', Summary (3 devices) at 0x105584d30),\n",
-       "             ('Bus', Bus (5 devices) at 0x1056110d0),\n",
-       "             ('PQ', PQ (3 devices) at 0x12f9b8df0),\n",
-       "             ('PV', PV (3 devices) at 0x12f9caa60),\n",
-       "             ('Slack', Slack (1 device) at 0x12f9e0910),\n",
-       "             ('Shunt', Shunt (0 devices) at 0x12f9eb3d0),\n",
-       "             ('Line', Line (7 devices) at 0x12f9eb880),\n",
-       "             ('PVD1', PVD1 (0 devices) at 0x12f9f4f70),\n",
-       "             ('ESD1', ESD1 (0 devices) at 0x12fa065b0),\n",
-       "             ('REGCA1', REGCA1 (0 devices) at 0x12fa06b20),\n",
-       "             ('REGCV1', REGCV1 (0 devices) at 0x12fa11160),\n",
-       "             ('REGCV2', REGCV2 (0 devices) at 0x12fa11940),\n",
-       "             ('Area', Area (3 devices) at 0x12fa11e80),\n",
-       "             ('Region', Region (2 devices) at 0x12fa1e640),\n",
-       "             ('SFR', SFR (2 devices) at 0x12fa1edf0),\n",
-       "             ('SR', SR (2 devices) at 0x12fa2e490),\n",
-       "             ('NSR', NSR (2 devices) at 0x12fa2e8b0),\n",
-       "             ('VSGR', VSGR (0 devices) at 0x12fa2ecd0),\n",
-       "             ('GCost', GCost (4 devices) at 0x12fa3a160),\n",
-       "             ('SFRCost', SFRCost (4 devices) at 0x12fa3a7f0),\n",
-       "             ('SRCost', SRCost (4 devices) at 0x12fa3ad90),\n",
-       "             ('NSRCost', NSRCost (4 devices) at 0x12fa471f0),\n",
-       "             ('VSGCost', VSGCost (0 devices) at 0x12fa47610),\n",
-       "             ('DCost', DCost (3 devices) at 0x12fa47910),\n",
-       "             ('TimeSlot', TimeSlot (0 devices) at 0x12fa47e80),\n",
-       "             ('EDTSlot', EDTSlot (24 devices) at 0x12fa50940),\n",
-       "             ('UCTSlot', UCTSlot (24 devices) at 0x12fa50d60)])"
+       "OrderedDict([('Summary', Summary (3 devices) at 0x1102ec910),\n",
+       "             ('Bus', Bus (5 devices) at 0x11001f6a0),\n",
+       "             ('PQ', PQ (3 devices) at 0x14cf7a490),\n",
+       "             ('PV', PV (3 devices) at 0x137ae0100),\n",
+       "             ('Slack', Slack (1 device) at 0x14cf7d610),\n",
+       "             ('Shunt', Shunt (0 devices) at 0x14cfa14c0),\n",
+       "             ('Line', Line (7 devices) at 0x14cfa1970),\n",
+       "             ('PVD1', PVD1 (0 devices) at 0x14cfbb0a0),\n",
+       "             ('ESD1', ESD1 (0 devices) at 0x14cfbb6a0),\n",
+       "             ('REGCA1', REGCA1 (0 devices) at 0x14cfbbc10),\n",
+       "             ('REGCV1', REGCV1 (0 devices) at 0x14cfc5250),\n",
+       "             ('REGCV2', REGCV2 (0 devices) at 0x14cfc5a30),\n",
+       "             ('Area', Area (3 devices) at 0x14cfc5f70),\n",
+       "             ('Region', Region (2 devices) at 0x14cfd3730),\n",
+       "             ('SFR', SFR (2 devices) at 0x14cfd3ee0),\n",
+       "             ('SR', SR (2 devices) at 0x14cfde580),\n",
+       "             ('NSR', NSR (2 devices) at 0x14cfde9a0),\n",
+       "             ('VSGR', VSGR (0 devices) at 0x14cfdedc0),\n",
+       "             ('GCost', GCost (4 devices) at 0x15e5de250),\n",
+       "             ('SFRCost', SFRCost (4 devices) at 0x15e5de8e0),\n",
+       "             ('SRCost', SRCost (4 devices) at 0x15e5dee80),\n",
+       "             ('NSRCost', NSRCost (4 devices) at 0x15e5ec2e0),\n",
+       "             ('VSGCost', VSGCost (0 devices) at 0x15e5ec700),\n",
+       "             ('DCost', DCost (3 devices) at 0x15e5eca00),\n",
+       "             ('TimeSlot', TimeSlot (0 devices) at 0x15e5ecf70),\n",
+       "             ('EDTSlot', EDTSlot (24 devices) at 0x15e5f5a30),\n",
+       "             ('UCTSlot', UCTSlot (24 devices) at 0x15e5f5e50)])"
       ]
      },
      "execution_count": 5,
@@ -269,7 +269,7 @@
        "      <td>PQ_1</td>\n",
        "      <td>1.0</td>\n",
        "      <td>PQ 1</td>\n",
-       "      <td>1</td>\n",
+       "      <td>Bus_2</td>\n",
        "      <td>230.0</td>\n",
        "      <td>3.0</td>\n",
        "      <td>0.9861</td>\n",
@@ -283,7 +283,7 @@
        "      <td>PQ_2</td>\n",
        "      <td>1.0</td>\n",
        "      <td>PQ 2</td>\n",
-       "      <td>2</td>\n",
+       "      <td>Bus_3</td>\n",
        "      <td>230.0</td>\n",
        "      <td>3.0</td>\n",
        "      <td>0.9861</td>\n",
@@ -297,7 +297,7 @@
        "      <td>PQ_3</td>\n",
        "      <td>1.0</td>\n",
        "      <td>PQ 3</td>\n",
-       "      <td>3</td>\n",
+       "      <td>Bus_4</td>\n",
        "      <td>230.0</td>\n",
        "      <td>4.0</td>\n",
        "      <td>1.3147</td>\n",
@@ -311,11 +311,11 @@
        "</div>"
       ],
       "text/plain": [
-       "      idx    u  name  bus     Vn   p0      q0  vmax  vmin owner  ctrl\n",
-       "uid                                                                  \n",
-       "0    PQ_1  1.0  PQ 1    1  230.0  3.0  0.9861   1.1   0.9  None   1.0\n",
-       "1    PQ_2  1.0  PQ 2    2  230.0  3.0  0.9861   1.1   0.9  None   1.0\n",
-       "2    PQ_3  1.0  PQ 3    3  230.0  4.0  1.3147   1.1   0.9  None   1.0"
+       "      idx    u  name    bus     Vn   p0      q0  vmax  vmin owner  ctrl\n",
+       "uid                                                                    \n",
+       "0    PQ_1  1.0  PQ 1  Bus_2  230.0  3.0  0.9861   1.1   0.9  None   1.0\n",
+       "1    PQ_2  1.0  PQ 2  Bus_3  230.0  3.0  0.9861   1.1   0.9  None   1.0\n",
+       "2    PQ_3  1.0  PQ 3  Bus_4  230.0  4.0  1.3147   1.1   0.9  None   1.0"
       ]
      },
      "execution_count": 6,
@@ -343,23 +343,23 @@
     {
      "data": {
       "text/plain": [
-       "OrderedDict([('DCPF', DCPF at 0x12f9b8490),\n",
-       "             ('PFlow', PFlow at 0x12fa5fa00),\n",
-       "             ('CPF', CPF at 0x12fa73070),\n",
-       "             ('ACOPF', ACOPF at 0x12fa736a0),\n",
-       "             ('DCOPF', DCOPF at 0x12fa73fa0),\n",
-       "             ('ED', ED at 0x12fca9100),\n",
-       "             ('EDDG', EDDG at 0x12fcb40a0),\n",
-       "             ('EDES', EDES at 0x12fcc7ac0),\n",
-       "             ('RTED', RTED at 0x12fe09fd0),\n",
-       "             ('RTEDDG', RTEDDG at 0x12fe1c0d0),\n",
-       "             ('RTEDES', RTEDES at 0x12fe42760),\n",
-       "             ('RTEDVIS', RTEDVIS at 0x12fe684f0),\n",
-       "             ('UC', UC at 0x12fe7ac40),\n",
-       "             ('UCDG', UCDG at 0x160845430),\n",
-       "             ('UCES', UCES at 0x160866370),\n",
-       "             ('DOPF', DOPF at 0x16088dd60),\n",
-       "             ('DOPFVIS', DOPFVIS at 0x1608b0070)])"
+       "OrderedDict([('DCPF', DCPF at 0x1102eb970),\n",
+       "             ('PFlow', PFlow at 0x15e60d3a0),\n",
+       "             ('CPF', CPF at 0x15e60d910),\n",
+       "             ('ACOPF', ACOPF at 0x15e632a00),\n",
+       "             ('DCOPF', DCOPF at 0x15e64f160),\n",
+       "             ('ED', ED at 0x15e6901c0),\n",
+       "             ('EDDG', EDDG at 0x15e688040),\n",
+       "             ('EDES', EDES at 0x15e60ce50),\n",
+       "             ('RTED', RTED at 0x15e6b8460),\n",
+       "             ('RTEDDG', RTEDDG at 0x15e6b8520),\n",
+       "             ('RTEDES', RTEDES at 0x15e6dbbb0),\n",
+       "             ('RTEDVIS', RTEDVIS at 0x15e6ff940),\n",
+       "             ('UC', UC at 0x162648400),\n",
+       "             ('UCDG', UCDG at 0x16307a490),\n",
+       "             ('UCES', UCES at 0x16309f3d0),\n",
+       "             ('DOPF', DOPF at 0x1630c2dc0),\n",
+       "             ('DOPFVIS', DOPFVIS at 0x1630e60d0)])"
       ]
      },
      "execution_count": 7,
@@ -396,7 +396,7 @@
      "name": "stderr",
      "output_type": "stream",
      "text": [
-      "Routine <RTED> initialized in 0.0130 seconds.\n"
+      "Routine <RTED> initialized in 0.0139 seconds.\n"
      ]
     },
     {
@@ -466,7 +466,7 @@
      "name": "stderr",
      "output_type": "stream",
      "text": [
-      "RTED solved as optimal in 0.0173 seconds, converged after 9 iterations using solver ECOS.\n"
+      "RTED solved as optimal in 0.0207 seconds, converged after 9 iterations using solver ECOS.\n"
      ]
     },
     {