fix: change TOML config file to use MD

.github/workflows/semantic-release.yml

@@ -17,7 +17,6 @@ jobs:
     permissions:
       id-token: write
       contents: write
-      pull-requests: write
 
     steps:
     - name: Harden Runner
@@ -40,27 +39,8 @@ jobs:
       run: |
         echo "short_sha=$(git rev-parse --short HEAD)\n" >> $GITHUB_OUTPUT
 
-    - name: Action | Check if release is needed
-      id: check
-      # Adjust tag with desired version if applicable.
-      uses: python-semantic-release/python-semantic-release@c1bcfdbb994243ac7cf419365d5894d6bfb2950e # v9.12.0
-      with:
-        github_token: ${{ secrets.GITHUB_TOKEN }}
-        git_committer_name: "github-actions"
-        git_committer_email: "[email protected]"
-        root_options: -vv --noop
-        build: false
-        changelog: true
-        commit: false
-        push: false
-        tag: false
-        vcs_release: false
-        # prerelease: true
-        # build_metadata: ${{ github.ref_name }}@${{ steps.vars.outputs.short_sha }}
-
     - name: Action | Semantic Release - Update version
       id: release
-      if: steps.check.outputs.released == 'true'
       # Adjust tag with desired version if applicable.
       uses: python-semantic-release/python-semantic-release@c1bcfdbb994243ac7cf419365d5894d6bfb2950e # v9.12.0
       with:
@@ -73,20 +53,3 @@ jobs:
         push: true
         tag: true
         vcs_release: false
-        prerelease: true
-        prerelease_token: rc
-        build_metadata: ${{ steps.vars.outputs.short_sha }}
-
-    - name: Action | Create Pull Request - Release
-      if: steps.check.outputs.released == 'true'
-      run: |
-        gh pr create -B main -H staging --title "release: Merge into main and create tag as v${{ steps.release.outputs.version }}" --body 'Created by Github action: semantic-release.yml'
-      env:
-        GITHUB_TOKEN: ${{ secrets.GITHUB_TOKEN }}
-
-    - name: Action | Create Pull Request - Chore
-      if: steps.check.outputs.released == 'false'
-      run: |
-        gh pr create -B main -H staging --title 'chore: Merge non-code changes into main' --body 'Created by Github action: semantic-release.yml'
-      env:
-        GITHUB_TOKEN: ${{ secrets.GITHUB_TOKEN }}

pyproject.toml

@@ -77,7 +77,7 @@ sansmic = "src/python/sansmic"
 [tool.semantic_release]
 assets = []
 build_command_env = []
-commit_message = "release: {version}\n\nAutomatically generated by python-semantic-release"
+commit_message = "chore: update version text to {version}\n\nAutomatically generated by python-semantic-release"
 commit_parser = "angular"
 logging_use_named_masks = false
 major_on_zero = true

src/ext_modules/libsansmic/libsansmic.cpp

@@ -22,14 +22,12 @@ PYBIND11_MODULE(libsansmic, m) {
 
   py::enum_<sansmic::LeachMode>(m, "CRunMode",
                                 "See :py:class:`sansmic.model.SimulationMode`.")
-      .value("ORDINARY", sansmic::LeachMode::Ordinary,
+      .value("ORDINARY", sansmic::LeachMode::ORDINARY,
              "ordinary leaching (water in, brine out)")
-      .value("WITHDRAWAL", sansmic::LeachMode::Withdrawal,
+      .value("WITHDRAWAL", sansmic::LeachMode::WITHDRAWAL,
              "oil withdrawal (water in, oil out)")
-      .value("LEACH_FILL", sansmic::LeachMode::LeachFill,
+      .value("LEACH_FILL", sansmic::LeachMode::LEACH_FILL,
              "leach and fill (water and oil in, brine out)")
-      .value("OIL_FILL", sansmic::LeachMode::OilFill,
-             "oil fill (oil in, brine out)")
       .export_values();
 
   py::enum_<sansmic::GeomFormat>(

src/ext_modules/libsansmic/libsansmic.hpp

@@ -67,10 +67,9 @@ const int UNIMPLEMENTED_GEOMETRY_IDATA =
 
 /// @brief The leaching operations mode for sansmic.
 enum LeachMode : int {
-  Ordinary = 0,    //!< fill with raw water, produce brine
-  Withdrawal = 1,  //!< fill with raw water, produce oil
-  LeachFill = 2,   //!< fill with oil and raw water, produce brine
-  OilFill = -1     //!< fill with oil, produce brine
+  ORDINARY = 0,    //!< fill with raw water, produce brine
+  WITHDRAWAL = 1,  //!< fill with raw water, produce oil
+  LEACH_FILL = 2,   //!< fill with oil and raw water, produce brine
 };
 
 /// @brief The format of the data; will go away once python code fully handles

src/ext_modules/libsansmic/model.cpp

@@ -334,21 +334,16 @@ int sansmic::Model::init_stage(void) {
     z_obi_stop = -double(stopCriteria);
   }
 
-  // if the current depths are below zero (?) set to the
-  // height of the insolubles plus the absolute height given
-  // I.e., consider that these are relative heights above the
-  // level of the insoluble materials not absolute heights.
+  // Version 1.1.0: removed relative heights above new floor height as negatives
+  // Version 1.1.0: Negative values will be considered depths below surface
   if (h_inj < 0) {
-    h_inj = h_insol - h_inj;
+    h_inj = z_TD0 + h_inj;
   }
   if (h_prd < 0) {
-    h_prd = h_insol - h_prd;
+    h_prd = z_TD0 + h_prd;
   }
   if (h_obi < 0) {
-    h_obi = h_insol - h_obi;
-  }
-  if (h_uso < 0) {
-    h_uso = h_insol - h_uso;
+    h_obi = z_TD0 + h_obi;
   }
 
   // use previous OBI if OBI is ~0
@@ -401,7 +396,7 @@ int sansmic::Model::init_stage(void) {
     C_cav[n_nodes] = C_hat;
     C_cavAve = C_cav0;
 
-    if (runMode == Withdrawal) {
+    if (runMode == WITHDRAWAL) {
       dt_min = (_pi_ * sq(r_cavMin) * dz) / (Q_in + 1.0e-10);
       if (dt_min < 0.01) {
         dt_min = 0.01;
@@ -415,7 +410,7 @@ int sansmic::Model::init_stage(void) {
       f_disSav[i] = f_dis[i];
     }
     // FIXME: do we really want this next line?
-    if (runMode == Withdrawal && C_cav0 > 1.0) {
+    if (runMode == WITHDRAWAL && C_cav0 > 1.0) {
       std::fill(C_cav.begin(), C_cav.end(), C_cav0);
       C_cav[n_nodes] = C_hat;
       C_cavAve = C_cav0;
@@ -449,7 +444,7 @@ int sansmic::Model::init_stage(void) {
   // End of initialization of cavern settings
 
   // set the prod and min timestep if withdrawal leach
-  if (runMode == Withdrawal) {
+  if (runMode == WITHDRAWAL) {
     prodCell = obiCell;
     dt_min = (_pi_ * sq(r_cavMin) * dz) / (Q_in + 1.0e-10);
     // next two lines are commented out?
@@ -575,6 +570,8 @@ int sansmic::Model::leach() {
     throw sansmic::UNIMPLEMENTED_FLOW_TABLES;
   }
 
+  double t_add = 0;
+
   // Convert back to BPD? Ugh.
   Q_inBPD = Q_in * cf_to_bbl * per_h_to_per_d;
   Q_fillBPD = Q_fill * cf_to_bbl * per_h_to_per_d;
@@ -707,7 +704,7 @@ int sansmic::Model::leach() {
   // end of adjust the plume model (reverse)
 
   // leach fill from production to OBI
-  if (runMode >= LeachFill) {
+  if (runMode >= LEACH_FILL) {
     for (int i = prodCell; i <= obiCell; i++) {
       if (i > maxProdOrJet) {
         V_injSigned[i] = 0.0;
@@ -782,7 +779,7 @@ int sansmic::Model::leach() {
     if (i < minProdOrJet || i > maxProdOrJet) {
       V_injSigned[i] = 0.0;
     }
-    if (i > maxProdOrJet && runMode == LeachFill) {
+    if (i > maxProdOrJet && runMode == LEACH_FILL) {
       V_injSigned[i] = -Q_fill;
     }
     r = max(r_cav[i], 1.0e-10);
@@ -1086,14 +1083,14 @@ int sansmic::Model::leach() {
 
   izbs = obiCell;
   // move OBI if not Ordinary leaching mode
-  if (runMode == LeachFill) {
+  if (runMode == LEACH_FILL) {
     // move OBI if simultaneous LeachFill
     i_obi = int(h_obi / dz) + 1;
     dz_inc = Q_fill * dt / (_pi_ * sq(r_cav[i_obi]));
     h_obi = h_obi - min(dz_inc, dz);
     obiCell = int(h_obi / dz + 0.5) + 1;
     obiCellBelow = obiCell - 1;
-  } else if (runMode != Ordinary) {
+  } else if (runMode != ORDINARY) {
     // move OBI if Withdrawal or OilFill
     i_obiOld = obiCell;
     i_obi = int(h_obi / dz) + 1;
@@ -1115,9 +1112,9 @@ int sansmic::Model::leach() {
 
   // CALCULATE MASS BALANCE CORRECTION FACTOR
   m_brineNew = m_brineNew - V_insol * C_cav[1];
-  if (runMode == Ordinary) {
+  if (runMode == ORDINARY) {
     Q_fill = 0.0;
-  } else if (runMode == Withdrawal) {
+  } else if (runMode == WITHDRAWAL) {
     Q_fill = -ddim(Q_out, 0.0);
   }
   p5 = Q_fill;
@@ -1205,11 +1202,13 @@ int sansmic::Model::leach() {
     if (b_is_injecting) {
       if (abs(z_obi - z_obi_stop) < 0.1 * dz) {
         t_end = t;
-      } else if (runMode != LeachFill && z_obi < z_obi_stop) {
+      } else if (runMode == WITHDRAWAL && z_obi <= z_obi_stop) {
         t_end = t;
-      } else if (z_obi > z_obi_stop) {
+      } else if (runMode == LEACH_FILL && z_obi >= z_obi_stop) {
         t_end = t;
       }
+      // dbh: there probably ought to be an exception check for ordinary
+      // mode, but the OBI doesn't move so it should be impossible to reach
     }
   }
   // stop on time - clear the handling variables

src/ext_modules/libsansmic/stage.cpp

@@ -22,7 +22,7 @@
  */
 sansmic::Stage::Stage() {
   title = "";
-  leach_mode = Withdrawal;
+  leach_mode = WITHDRAWAL;
   print_freq = -1;
   is_subsequent = 0;
   t_rest = -1;

src/python/sansmic/io.py

@@ -335,11 +335,18 @@ def read_dat(str_or_buffer: Union[str, Path], *, ignore_errors=False) -> Scenari
             stage.stop_value = float(stop_value)
             if stage.stop_value < 0:
                 stage.stop_condition = StopCondition.DEPTH
-            if stage.stop_value > 0:
+                stage.stop_value = scenario.floor_depth + stage.stop_value
+            elif stage.stop_value > 0:
                 stage.stop_condition = StopCondition.VOLUME
-            stage.brine_injection_depth = float(injection_height)
-            stage.brine_production_depth = float(production_height)
-            stage.brine_interface_depth = float(interface_height)
+            stage.brine_injection_depth = scenario.floor_depth - float(injection_height)
+            stage.brine_production_depth = scenario.floor_depth - float(
+                production_height
+            )
+            stage.brine_interface_depth = (
+                scenario.floor_depth - float(interface_height)
+                if float(interface_height) != 0
+                else 0
+            )
             stage.brine_injection_rate = float(injection_rate)
             stage.inner_tbg_inside_diam = float(inn_tbg_inside_radius) * 2
             stage.inner_tbg_outside_diam = float(inn_tbg_outside_radius) * 2